Random unit models and textures for rebel troopers to give the variety of species they had in the movie and to make them a slightly more ragtag force (which is the reason they're so cool)
Veterancy. Especially for the rebels. While the imperials have a bunch of cannon fodder, for the small rebel alliance individual troops and pilots are important. It would be cool if as they gained rank their skins changed (gaining medals etc and prehaps personalising their fighters like the Yavin X-wings) and used different animations (fighters might pull off some cool maneuvers while troops might be able to do stuff like say... melee (this sounds silly but I'm thinking of that rebel commando punching that imperial officer in ROTJ)
It'd be nice for the Imperials to have extremely experienced star destroyer captains and AT-ATs. I know there probably wont be individual upgrades like BFME, but it would be nice to give your best captain the best ship. (I dont mean anything complicated like giving ships individual pilots and captains... when I refer to captain or pilots I merely mean a capital ship or fighter unit)
Different stormtrooper armour for different enviroments. Merely eye candy, but it'd be nice to have sand troopers on Tatooine or snowtroopers on hoth. Not sure how you'd fit scout troopers in as they're more of their own unit type. It'd be a nice nod to the JK series if prehaps they added swamptroopers in a jungle environment. No stats change, simply a different model. Same for the rebels.
On the subject of stormtroopers, a zero-g stormtrooper from the Xwing series would be fun for space battles.
Anti Air. I've hated the way both force commander and Galactic battlegrounds did anti-air. Firstly air units were so weak against it made it useless. Seccondly, both flak and giant missiles are quite un-starwarsy. In FC troops could simply fire up at aircraft. It seems like we might not see any air units on the ground except for strafing runs, there is however the case of the snowspeeder. I'd quite like the AT-AA to make a return (It was in FC.. I'm not sure if it existed in EU before that but it returned for GB albeit with silly red missiles stuck on it) as well as it was a nice addition to the walker arsenal. So I suggest that any unit for which it is logical can shoot at aircraft. So troops can point their guns up and fire, AT-ATs can look up and fire, tanks can swivel their turrets up and fire, an AT-ST can't because it's head doesn't seem able to rotate that far. The AT-AA could be a specific anti air unit and be quite powerful against aircraft.
The best counter for aircraft should be other aircraft. This is going purely from the films of course..
Colliding capital ships. I love the scene in ESB where two huge star destroyers almost crash.. it'd be cool if we could trick ships into doing this.. or even order them to execute rams! It would also be cool if a ship, no matter what size could possibly go out of control when being destroyed (Kinda like the troll and mumakil in BFME) smashing into friend and foe alike (No 1 lesson learnt in SW: Raise the shields BEFORE the A-Wing hits the bridge)
Fighters are too small most of the time to be hit by turbolasers. A star destroyer would have a hard time hitting fighters buzzing around it, and the best counter would be to launch your own fighters.
Proper shield generators. I've mentioned it before but it's always been a disapointment in the last few games that shields merely raise the HP of units. They should simply deflect fire coming from the outside. Once units are within the shields they can fire away to their hearts content.
Moving while firing. This was the one advantage FC had over GB. Units actually advanced while firing. The limitations of the GB engine meant that troops would march up and stand still while firing. There was an interview before CC saying that in CC you would be able to move and fire... but I think it was cut. Anyway.. it'd be nice for units to be able to advance and fire at the same time.
<End force Long post>
"Your life does flash before your eyes before you die..... the process is called LIVING"