Having now played two more games, I’ll expand on my thoughts.
Once you know what you are doing, humanity can win. The balance favors the cylons, but not outrageously so. On the downside, that’s due to random variability. We had a five player game with no cylons until the midpoint where the cylons won, and a 6 player game with an early cylon that the humans won easily. The main difference appeared to be due to the crisis deck. In the second game, 3 players were constantly scouting/peeking to make sure that the horrible cards got bypassed, leaving only the routinely bad cards.
More potential flaws — There are significant turn order effects. Often a cylons best bet is to play naturally, then let loose on the turn just prior to theirs. If your Right Hand Opponent draws an ugly crisis, just drop your hand to ensure that humanity fails, then reveal as a cylon on your turn. But if your LHO draws that crisis, dumping your hand reveals you, and you get sent to the brig. If the cylons sit back-to-back, then they can coordinate their ships much better. If this is true, then you are again at the mercy of the deal. That’s forgivable in a shorter game.
Both games peaked a bit early — the ending was clear a few turns before it happened. We probably spent 4.5 hours on two games (one of which included ~15 minutes of rules), which wasn’t bad but could be better. I think having an agreement to let teams concede will probably help.
The humans could have conceded in the first game, and the cylons in the last and shaved a few player turns.
[I'm pro-concession in general in two player/team games, but it's a touchy issue.]
The other issue is that the balance probably changes based on # of players. 5 players have 60% of the 2nd half turns pro-human. 6 Player games are 50% or 66%, depending on how the sympathizer turns out. So it’s in the humans interest to throw a bit to make sure that the sympathizer is pro-human. Still early to claim balance issues, but the niggling doubt is there that this is a 2 hour game to resolve a random shuffle of some cards…
My overall impression is still favorable, though.
Update: I agree with Alexfrog’s comments below. I don’t have enough experience yet; but he adds more data points. It bugs me that revealed cylons can add skill cards, too. That’s just not thematic. (Perhaps a revealed sympathizer could add skill cards, to balance not being able to direct the fleet). I’d go so far as to say that once all cylons are revealed, the destiny deck goes away (or the cards flip face up, perhaps).
As for balance, I still like the sleeper phase, but I think that you should ensure that both cylons aren’t in the opening. Or perhaps cylons can’t take their “Reveal” action until after the sleeper phase. Just to reduce variability.
My game length suggestion is that revealed cylons taking the caprica action don’t get to skip the jump drive step, but do skip the activate ships step. They get to pick two, so they’ll still usually not have to deal with advancing the jump drive, but the game won’t completely stall. Cylons activating their fleet don’t cause the jump to cycle. Alternately, you could make all cylon turns roll a die for the jump drive. Maybe 1-3, jump advances.
I started a BGG thread on variants.
You know what movie needs a BSG-style game? The Thing (or Who Goes There, for purists). You start with one thing, then he can infect others and if they get a majority, they win. How to do this without it become a pure werewolf thing is left as an exercise for the designer.