Windu - I agree with what you're saying, but I think in order for this Conquer the Galaxy idea to work, you'll have to take some liberties. Sure, Kamino isn't even in the Republic, but it is the planet from which the army issues forth. Plus it is recognisable from the movies which I think is important.
And yes, Geonosis was captures in Episode II, but it still is the starting planet for the Confederacy because that is how it is in the movies. If you're using that argument you could also say that Alderaan was destroyed by the Empire so can't be used in the game. Think of it this way: they are playing Conquer the Galaxy in Episode II and the Republic player captures the Confederacy player's homeworld. Again, it is also recognisable from the movies.