That could work well. If we're allowing the Empire to fight the Republic I guess it won't matter that neither of them start on Coruscant.
I'd suggest Kamino for the Republic (since that's where their army was initially built) and perhaps Kuat for the Empire (not Corellia because as I understand my EU they weren't exactly the most Imperialistic planet).
So I'd suggest the following for starting planets:
Rebels: Yavin 4
Trade Federation: Neimoidia
Not sure what you'd do for the Vong, don't they come from another galaxy?
As for benefits that planets give you, I'd suggest they only give you economic bonuses or bonus units, though admittedly I'm not 100% clear on how the Conquer the Galaxy thing works. Here's my ideas (note that planets which are the homeworld for a civ will still give the bonuses, which makes them even more attractive to capture:
Bespin: Weapon upgrades are cheaper because of the Tibanna gas mine
Coruscant: Huge economic bonuses, perhaps like a constant flow of resources.
Dagobah: Jedi are cheaper?
Endor: Bonus Ewok units such as trappers and such.
Geonosis: Mechanical units built faster
Kamino: Biological units built faster
Kuat: Aircraft are built faster
Naboo: Power sources such as Power Cores are cheaper due to use of Naboo Plasma
Neimoidia: Trade techs are cheaper
Not sure of any others.