The "identity crisis" the Federation might face is exactly the kind of thing I think of when I talk about "ethical exploration" as a primary theme of Star Trek. It's the question that goes right to the heart of any individual or group: Who are you when it really counts? The best gameplay I've ever experienced (and the best SF I've ever read, for that matter) has been driven by that level of humanistic storytelling. I'd love to see it play a major role in guiding the gameplay of Star Trek Online.
Actually, to take a step back for a moment, it's interesting that we all seem to be good with the idea that a Serious Threat to the Federation will be part of the game. It's not a requirement; you can make a perfectly good MMORPG without imposing some Looming Disaster... but it does seem like a pretty obvious idea, doesn't it?
If Star Trek Online's developer is thinking along these lines, then the big question is whether they're thinking mostly internal or external. External threats (the Dominion War) are great for slam-bang action. Internal threats (Section 31) are superb for meaningful story-driven roleplaying.
But maybe there's a threat that's both internal and external? Something that could drive both action and story in a massively multiplayer game for years to come...?
Me, I like the idea of a critical technology (such as warp drive or replicators) going kerflooey and the barbarians banging on the gates to take advantage of the problem, but that's me. I could easily go along with the Eugenics Wars Part II as long as this internal threat also had some external component.
And frankly, I'm still waiting for those darned neural parasites from TNG's "Conspiracy" to make their long-awaited reappearance. Maybe a civil war is fomented from inside the Federation itself.... (cue the spooky music)