I'm surprised that so many people think the CIS are the worst.
Here's how I see it stacking up:
Assault: Pretty much all the same, except for SBD, which I think is a great unit and is better than the rest.
Heavy Weapons: Pretty much all the same. Rebs get the 2 shot advantage, though.
Pilot (on foot): CIS/Empire- sucks. Rebs- Gun good in some situations, bad in others, I don't like it. Clones: Haven't experimented with the gun enough to judge.
Sniper- Rebs/ Droids have the extra zoom, which IMO is the only thing that makes snipers even remotely useful in this game.
Wookiee smuggler- Don't like it. Time bomb has limited uses, slow weapons, big ugly wookiee makes good target.
Jet Trooper- haven't played a whole lot, but seems pretty good, despite slow primary weapon.
Dark Trooper- Sucks. Sucks I hate it. It sucks.
Droideka- only special unit I actually am ever inclined to use. Has strengths and weaknesses, fun to use, not as easy as it looks.
Overall, I'd say it's pretty balanced, and I don't see what sucks about CIS. If it all comes down to Special unit, as some say, then I say Empire loses hands down.
Dark trooper sucks.
God is a placebo with nasty side effects.