I think I get what you're saying, and I agree with everything except I think two factions might be better. The third seems a bit out of place to me. Maybe we should just make the aliens and pit them against Omega's military? Maybe we can even fix his animations.
Anyway, here's what I've come up with in the past couple minutes:
Aliens:
* Landing Craft - main building, can morph between land and air
o Robot - worker unit
+ Generator - increases population cap
+ //barracks
# Gunner - alien with a ray gun
# Power Suit (requires Factory) - an alien in powered armor
+ Factory - builds mechanical units
# Killbot - robot with strong melee
# Mech - an alien in a mech, shoots rockets
# Tripod - a "War of the Worlds"-style walker with a heat ray
+ Space Port - calls in flying saucers
# Saucer - slow but tough air unit
Humans:
* Command Base
o Worker - hard-working guy with a hard hat, chainsaw, and jackhammer
+ Barracks
# Rifleman - soldier with an M-1 Garand
# RPG Trooper - soldier with a rocket launcher
# Gunner - soldier with a machine gun
+ Garage
# Humvee
# Sherman
# Hover Tank (requires Area 51)
+ Area 51 - examines alien technologies
# Scientist
* //upgrades go here
# Rocket Ship
# Rocket Ranger - soldier with a jet pack and ray gun