Yes, we had to pay for...wait for it...NEW RACES. And having purchased multiple copies of the previous games and expansions for myself and friends excuse me if I feel a bit miffed that the races in previous games weren't included.
Except at the end of GC II and all of its expansions, there were 12 factions. Expecting a brand new game to have ALL of those factions with unique tech trees and ship styles and other things is, frankly, unrealistic. Hell, custom tech trees wasn't even in the base game for GC II from what I understand. The fact that GC III has unique(ish) tech trees for each faction puts it leaps and bounds ahead of the base game for GC II.
And I keep mentioning the base game because comparing this to a fully expanded game at the end of its life just isn't fair. GC III has more things in it at is base game than GC II did. GC II did have a couple of more factions at launch. But since they didn't have unique trees, it's a bit of an apples and oranges comparison. As a side point, last I heard, the road map for GC III will be 16 total major factions (I don't know if this includes the Snathi Revenge or not). That will indeed put it beyond GC II.
Complaining about this is kinda like complaining about "new/old" factions appearing in the various iterations of Civilizations. I mean, one doesn't expect all of the features/factions of the last update of a Civ game to appear in a brand new version of the base game of Civ. Or at least one shouldn't, IMO.
Finally while I sympathize a bit on the "multiple copies" of the game bit, the fact is, this is a different game. This ISN'T GC II mk 2 update 3. It's a brand new game that builds upon the previous ones. Much like Civ 5 was different from Civ 4 was different from Civ 3.
Frankly if they didn't include more races from GC II that didn't make the cut at the beginning for whatever reason in expansions/DLC/updates, I'd be the one that was miffed.