(2) And also the rocket launcher is getting pretty boring. But now you can get more out of the rocket launcher by having a mine rocket launcher that shoots instead of 1 rocket it fires 5 small mine rocket's all at wone time with a deadly blow to the receiver . 
Note: Good point, but I'll be happy just as long as they put in the original Blaster launcher that allowed waypoints for the missile to travel.  (unedited. murphy=morph)

1) New weapons like a multiple missile launcher.  It might fire 4 or 5 missiles simultaneously, but each missile isn't as powerful as a single missile launcher!
2) Bigger bases. I hate those 18 squares to build bases! How about 21 or 24?
3) How about some new aliens?  Maybe a robot that fires miniature bombs
or a hovertank much like the humans!
4) A MUCH harder last mission!  Cydonia was one of the easiest missions I went on! I only had to kill 3 aliens in the whole 2-Part mission!
5) New weapons and technology!
6) Bigger, Badder Alien Bases! How about some 3 or 4 story bases? Make it  so the aliens chase after you though so you spend all day on a bug hunt!
7) Make it so you can see the soldiers you're about to hire!
8) SVGA Graphics and Better soundcard support! 
9) Tons of tile sets. You could have swamps where you're agents go waist deep in the water-It'll take 6 time units to move one space! Suddnely a new alien creature pops out of the water and spits it's corrosive venom all over you!  How about a city building where you start on the roof! You must take the stairs and shaft elevator to different levels
destroying the aliens!
10) Smart civilians!  Some of the civilians can have guns of their own! It be awesome to see one them pull out a rifle and shooting a sectiod in the ass!
Note: I agree with the more tilesets. I'd love a good swamp bug-hunt.

Now my wishes:

=> Combats in cities, underwater, in the artic, in deserts, jungles, etcetera, all in one game, like an XCom Saga.
=> First-person air combat, like those dogfight games.
=> multiple rocket/mine launcher both hand and vehicle ported
=> illuminating mines/grenades (like electroflares, chemical sticks), to be fired from these launchers.
=> A Flamethrower!
=> Stun grenades
=> Tatics research
=> More crafts
=> More space in the base
=> Something like a carrier ship, both performing as base and as a standard ship.
=> Night vision modes (perhaps attached to the armour...)
=> Covert operations mode, infiltration on a government, to discover if they are under alien influence...
Maybe all of this is unpossible to include in one game, but sure, it might inspire lots of other XCom sequels...

I have some suggestions of my own:
1.  specific sniper weapons (or at least custom-made weapons)
2.  APC's or Tanks that a can carry a passenger on top (perhaps with a turret).
3.  more battles in your own base (there's nothing like putting it all on the line on your home turf)
4.  the option of piloting Interceptor battles.

Switching gears, another battlescape scenario could be a world map like in XCOM I but then if the aliens attack or land in a city, the game would switch to XCOM apoc like cities.

Having the game turn-based is preferred but make it so people can't abuse the game ( like teleporting into an area and blowing it up and teleporting out ).  It should take more time units for an agent to do moves like that and/or include an editor so a game host can edit game settings like that or able to edit the aliens even.

The vehicles from XCOM apoc were excellent and would enjoy to see them return in XCOM 6.

One suggestion as to an agent's skill is the ability to break into an area, either through demolition or forcing an entry.  This would be like in the situation of breaking into an alien ship or if someone is helping the aliens and is barracaded in a building.

Lastly, multiplayer would be fun and the ability to play the alien's side would be quite fun.

2)  More varied races..  Possably many different alien factions rather than just one "enemy"  Many be even throw in a diffrernt human agency who are also interested in aquiring alien technology for themselves,, and don't mind bursting in on the scene..  "You may have shot this down,, but *WE* cleaned it out!!  It's ours I say by right of salvage!!"  THat should annoy a few X-Com commanders..  ;)

3)  More varied tech and tech trees..  One race might use something totally different from another,, but when combined make something entirely new.. Add a few problems thrown in as well..  After all,, these *are* usually experimental weapons!!  "This is  a sheild unit..  It will totally protect you from all sorts of attacks!!  Ummmm,, except for this one..  And maybe those two......" or  "Our nice new heavy SuperDuperThingy!!  It will kill the most powerful unit in the game with one shot!!  Errrr,, shame it won't damange anything else though........"
 

And those stupid civvys, simply GET IN THE WAY WHEN I AN TRYING TO KILL THAT DARNED SKELLY! Why can't they defend themselves or just simply scram???!!! Civilians telling us where the aliens are would be helpful too.

But after four X-COM and three Civ games, the rigid research tree, as great as it was, is getting a little tired.  Scientists in the real world poke around until they make a breakthrough - they don't know when it will happen or exactly what they'll find.

LEVEL A:  No Progress Bars. 

In X-COM Apocalypse, knowing exactly how long it was till you finished the project was kind of lame. Better, even, to have a certain percentage chance that the research completes every hour.  Projects would take the same average time, making the game consistent.  But sometimes your scientists would make a quick breakthrough, and sometimes you'd have to wait forever while they bumbled around the lab, not figuring things out... All the player knows is that they're working on it, nothing more. Civ felt like this even if it didn't work that way.

LEVEL B:  No Rigid Research Tree.

Your scientists work on a *category* of research, but what they discover is partially random.  For example, they work on "Biochemical warfare", but might discover toxins 1,2,or 3 - you don't know which.  And those toxins are pretty much the same power, but affect different aliens differently.  Toxins 4 and 5 (which are more powerful, but still each affect some aliens better than others) can't be discovered until you've discovered at least two of the first three, and toxin 6 (which affects all aliens and is very powerful) can't be discovered until you have both 4 and 5.   What's more, they might invent a toxin gun, or they might discover grenades that carry
the above toxins in gas form.  Which happens first changes each time you play.  Give 'em cool fake names like "picorotoxin" and "afthalotoxin" so people don't wonder why they discovered "toxin 2" before "toxin 1".

This forces you to think differently and use different  strategies  each time you play the game, which would be really cool, and more realistic to boot.  With a rigid tree, it's kind of boring playing the game a second time.

LEVEL C: Separate engineering from manufacturing.

The fact that you separated biochem from physics in X-COM Apoc was GREAT!  Three cheers to you; that was really cool.  Now try separating science and engineering and manufacturing.  This is even more complex, but could be pretty darn cool. 

Biochemists discover the toxins - not the weapons.  Physicists learn how plasma weapons work.  Then it's up to the engineers to
design the weapon that uses the technology.  How cool the weapon is depends on how much time they spend on it; you could make the stats of the first weapon they invent a little bit random, but if it's not as powerful, give it to them earlier on average.  If the engineers keep working on it, they will eventually invent better versions. Maybe their next toxigun is more accurate, or maybe it carries more ammunition.  Keep working at it and your third toxigun designed is more accurate, carries a lot of ammo, and fires faster. But to do spend this much time on it, you didn't have your engineers improving your armor, or plasma guns, or aircraft...

Once an item is designed by the engineers, the MANUFACTURING department now builds them.  This could even be non-human; an automated manufacturing center.  It could build anything, but only one at a time, and bigger or more complex things take longer.  Perhaps you have to build a bigger manufacturing machine to make big ships, etc.

1) Improved and more varying graphics; a return to the original's mood, ambiance and animated feel; being able to adjust screen size and resolution would be great as well.

2) Intelligent and proactive AI civvies, police, standard military (i.e. Reserves/Guard units) and gov't agencies (can be integrated nicely with suggestion no. 6 below);

3) More weapons (like shotguns, new beam weapons, flame throwers, multi-launchers, etc.) with far more variability;

4) New tech that is more represtentative of modern and future technology to start out with (i.e. night vision, soft body armor, sniper weapons, ghillie suits, etc.)  XCOM a multi-national force, something akin to JSOC/SOG/SOCOM with it's own special budget to get all the special goodies it will require just like any special forces command around the world;

5) Larger bases in both scalability but also in physical size for both good and bad guys, not to mention more options for features/equipment and placement options.  We should be able to place them on land, on water or under water as we deem necessary.

6) I would like to see more versatility with higher skill levels aside from the usual tougher, smarter opponents, and adding new dimensions to each new level in addition to the previous levels goodies... i.e: 
"Rookie" is just like the original's interface and complexity.
"Experienced" allows you to design and customize weapons.
"Veteran" gives you a dynamic tech tree and more seperated technologies such as Evan Dorn suggested.
"Master" would give you a more variable and real-world economy, much like Appocalypse.
"Diety" adds in the political variations of the global arena; maybe add in NATO or the UN as political entities to contend with aside from the various international governments and alliances.

7) Instead of battling a single alien force, why not have two alien forces battling over Earth, much like that of Starcraft.  As a result, you could play either of the alien forces or that of XCOM.  New and widely varied tech and aliens would great enhance replayability as well as providing more battles on more fronts!  Far more lethal and challenging.

8) I like the idea of first person, but I'd save it for a seperate game, it would make it a little messy for game play.  Maybe as an option for real-time (which I don't much care for anyway).  If it were done than hand to hand combat is a must, which means melee weapons would be a must.  I do like more versatility in UFO interception.  While doing a flight sim for interceptions is cool, it's just like turning missions into first person shooters.  If MicroProse could pull it off, including both would phenomenal!   Though logistically, it would be a nightmare.

9) Multi-player is a must!  Each player is a different commander for a different base!  Or force vs. force.  My compadre and I would love to see XCOM:UFO Def. as a multiplayer, even without any other modifications, and we'd be happy.  Are we easy to please or what?

1: While the ability to control the aliens was useful, wouldn't it be so much cooler if there was some way to make a group defect? Maybe through commincations from an alien ship to the base, or capturing a leader. Personally, I think it would add a very interesting new dimension to the game.

2: What's good for the goose... We always hear about the humans being taken away for some alien experiments, usually as a food product. Why not have rescue missions, as apposed to counter-terror acts. After all, ET has to know that if you kidnap the right person, there could be a signifigant gain.
 Of course, this could be how so many countries defected in the first two X-Coms.

3: Alright, we've heard about the andriods, and the mutants. But aside from a few minor stat changes (alright, maybe not *minor*, but not too impressive) they aren't very different from humans. Maybe there should be some noticable differances amongst the characters, or better yet, hesitation amongst the differing groups. After all, the AI's have been rejected by both normal humans and the altered mutants. Not much more than adding character within the game, but it would be a nice touch.

4: Random nearby items for civies to grab. Maybe just something like a baseball bat, or a pipe. Or there could be gun nuts, walking around with a hunting rifle and taking pot shots at aliens. Hell, have a few gangs go at it! I'd love to see the Crypts go after a squad of Sectoids.

5: Looking through the eyes of the trooper. If there's one thing that annoyed the hell out of me in all the X-Coms, it was just missing that alien when you're centered on a soldier, and loosing the trooper for it. So, maybe a small window could be added to show what that soldier is actually seeing. It wouldn't require much more than a rudimentary 3-D engine due to its size, and could give back
that creepy atmosphere the first two had.

6: Diplomacy. While the idea of multiple alien races is interesting, if it's all just scripted, the game would get real old after the first time. So maybe allowing for little tricks like peace treaties between factions, wars to break out amongst former allies, and all the neat little entriuge that goes on behind closed doors to occur would increase the game play.
    Or it might make the game too much like Master Of Orion. Still, having an alien ally every mission even if you "accidently" kill off all their soldiers would be more than a bit dull.

7: While we're on the topic of aliens, how about a few brand new races? Not rehashes of older ones, but something entirely new. Cybernetic beings that can hack into your crafts, or energy beings that absorb plasma, or psionic beasts that posess bodies for hosts?
    Alright, the last one kinda showed up. But I have yet to see anyone hack into my interceptor!

8: Separate "pro-alien" factions. Yes, I know that this was explored with Apocolypse, but not completely. If the Pro-Alien people were gathering weapons from the aliens, using their humanity to exhert pressure on other groups to cut funding to X-Com, then wouldn't that be a great deal harder to deal with than the occasional fanatic throwing him/herself on your gun?

9: Spies. Well, maybe not *spies*, but little trinkets like tracers for alien scouting ships, raiding parties, etc. Farther up the technological ladder, they could be made to explode on command, crippling ships, and killing aliens.

10: Communicaes between soldiers. Granted, with the shear number of troops that exist in the stratigic game, this little add on would be nearly impossible, if actual voices were used. But if you put in a little chat box, then you aviod that whole mess.
    And wouldn't you like to hear what that soldier is saying when he finally breaks down and decides to blow up half a city block?

11: Play as ET. It's been said before, and it will be said again. Imagine actually starting out with all those bizzare weapons, but only having a few Sectiods/Aquatoids/Whatevertiods to use as actuall troops. Then, having to actually find and build a colony before X-Com can find your ship. It would have to be an entirely different method of playing, because no one has ever found money
on any of the aliens. Troop detachments would be needed, as well as requistions for new weapons. Or maybe they'd just build them from the raw materials nearby.

12: Atmospheric conditions. Storms, Earthquakes, maybe even tidal waves would add a very different overall effect. All would disrupt communication, scaring both ET's and Squaddies allike, maybe even killing a few of both.

13: "Hand me that crowbar" Why is it when Aliens park their ships, they leave the doors unlocked? Why does everyone do that? I mean, when you send out a crew to repair your hull, and you know that the people that shot you down in the first place are comming, would you really want to leave your door unlocked? Super advanced technology, and the leave the front door open...

14: Basically, everything that's on Micheal Ivanoff's list. The man knows what he's talking about.

15: Maybe a few inside jokes... like having to deal with the MIB, or investigating a crashed Shuttlecraft... just something to break all the tense atmosphere, and make those times when you are wondering just where the last aliens is that much more spooky.
    Yeah, I can just picture having to watch the borg fight against a squad of Mutoids...
    "We are the borg. You will be assimilated. Resistance is futile"
    "GRRRAAH!" (translation: You have angered me and my comrades. Make your peace, for you go before the final judgement now.)
    (Firefight ensues, and little pieces of borg land everywhere)
    "Perhaps Resistance is not quite futile..."

16: Occasionally, there should be an Agent who has skills outside of just hunting bugs. Like say... enhancing that Laser Pistol over there, or peicemealing together some armor from the alien ship. Maybe even throwing their voice... As to how this would be actually implemented, I don't know. But it would be cool.