Shoulda known, it wasn't a matter of if but rather, a matter of when. Now, apparantly. Although, honestly, since Starcraft was based on land battles, there are very few examples of the various races' major ships. We are to assume all Zerg transportation is by overlord (although they doubtless infected their share of non-organic ships). And while the Protoss presumably have starships capable of leaving mass desolation (demonstrated by the Conclave's early tactic of annihilating infested planets, regardless of any humans in the way), we only see carriers and a handful of smaller craft in the Protoss fleet in SC. The United Earth Directorate (introduced in Brood War) and Mengsk's Terran Dominion may or may not merit being considered seperate but similar races for their tendency to squabble with each other In SC, they were the same in all things save their colors, but what would the SC universe be without space monkeys squabbling while aliens leave a trail of desolation? And a GalCiv2 mod would be a chance to differentiate them. I shouldn't have to add, but Zerg=evil. Protoss=good. Any and all space monkeys=neutral.
One last bit. You could also use the ingenious idea of seperate tech trees for each race from Alternate Universe, with custom races only able to go along one.