Eleazar: Your idea seems interesting, although the payoff takes long enough that planets with natives might not seem interesting/desirable.
Well, of course the goal is to be
interesting. The length of the delay and cost of uplift can be adjusted to make it worthwhile, but not so advantageous that keeping them is the only valid strategy. Xenophobic, or "Evil" empires should be able to exterminate the natives without ruining their chances to win.
I would suggest that if there are 'Artifacts' in the game, similar to the Oracle rewards in Heroes of Might and Magic, some artifacts might be discoverable by studying natives.
I'm only vaguely familiar with that game, perhaps you can explain more fully?