First off, I would recommend keeping it on PC. Its infinitely easier to maneuver large numbers of troops and such with a mouse than with analog sticks, at least in my opinion. It would also be far easier to capture screenshots and such.
As for obvious improvements...
1. Better graphics, duh.
2. Greater variety of units and such. Possibly limited customized Marines and Yautja.
3. Online play would be great!
4. Skirmish! I love doing those straight up fights without complicated objectives.
5. Level customization would be marvelous as well.
6. While I did greatly enjoy the wide variety of character classes, I would say that introducing new ones is a must if the sequel wants to improve further.
7. Although I didnt play with the aliens that much, I do have to agree with these other guys. They need a bigger population limit. While it was still impressive in the first game and almost impossible to fend of a full scale assault from a full size hive, it always seemed a bit too small... I would truly love to play a skirmish mode and fight off quite literally hundreds of swarming xenos! That is something to look forward too.
And yeah, the marines definitely need a bigger fighting force. At best, with a full population, they are a small platoon. Insufficient for combating yautja or xenomorph hives.
8. Preferably getting better close views, possibly even seeing from 1st person point of view. And being able to record battles and such would be marvelous, allowing for machinima!
Yes, Im a big fan of machinima, and would greatly like to do epic battles with AvP.
Other stuff would include
1. Customization. Marines are often divided up into large groups, ranging from squads, platoons, companies, battalions, and many others. You could have your own battalion with its own special numbers, color scheme, etc.
The same goes for yautja. Make your own clan style! Im not sure if it would work for aliens, but Im sure it would still work well.
2. Small character modifications. When playing as the Yautja, I was somewhat dissapointed that each warrior only got one weapon. What if you could give them a couple? A burner in one hand, spear in another in addition to a shoulder mounted weapon. Versatillity and stuff.
3. More weapons! I love the introduction of weapons in the first game, like the blazer and plasma glaive, but it could still be better. I know that the marines have plasma rifles, possibly railguns and other equipment. Let them use it! Same goes for Yautja. Let them have burner rifles and heavy weapons, at the cost of heavy price and other possible drawbacks. But it would suit the purpose marvelously!
4. Vehicles. I cant stress how vital these are to strategy games. An APC would be more than welcome for my marine squad, and possibly light assault vehicles, and drop ship bombing runs. The yautja could easily ships that could bombard from orbit. IE: That mighty big energy weapon that was used in the first AvP movie to blast that tunnel, or the bolts in AvP2 that blasted that marine ship.
5. One of the things that really irritated me in the first one was playing as aliens and not being able to produce eggs because there were others in the way. That bugged me sooooooo much! Id rather have them somehow get put further out and stuff.
I hope they do create a sequel, and that some of these suggestions are used.