When it comes time to do UU's, each Civ should get one land-based and one air-based, with the other units analogous to each other, for example:
Rebels..........Empire.........Yuuzhan Vong
E-Wing.........TIE Fighter...Coralskipper (Fighter units)
Y-Wing.........TIE Bomber...??? (Bomber units)
MC Cruiser.....ISD.............??? (Battleship-type units)
Rebel Soldier..Stormtrooper.YV Warrior
Sorry for the dots, they're just to illustrate the point and keep things relatively lined up.
UUs:
Rebels: Bothan Spy, X-Wing
Empire: Darktrooper, SSD
Yuuzhan Vong: Shamed One(Fast Worker-ish?), Worldship (souped-up carrier?)
The different classes of capital ships could be determined by the faction building them (bridging off a common path, maybe)
Galleon (Star Galleon)
Destroyer (Dreadnaught)
Cruiser (Bothan Assault Cruiser, Victory-class Star Destroyer)
Battleship (Mon Calamari Cruiser, Imperial-class Star Destroyer, Chiss Star Destroyer)
Hope that helps the future unit plans
I'd be glad to help with Civilopedia entries for the Chiss, the Vong or anything EU-ish you need, I tend to know more about the EU than the prequels.