My group plays with some of the Pegasus expansion (no Caprica board, but the Pegasus ship board) and the Exodus characters, extra loyalty cards, and skill cards but nothing else from Exodus (no cylon fleet, ionian nebula, or conflicted loyalty cards). We generally enjoy this mix, except...
One thing that our members are repeatedly finding is that most of the fun of the game is the paranoia induced by not knowing who the cylons are. However, our only real fear is what the cylon might do if they get a "great reveal," that is, being able to screw the humans with a combo of a failed skill check right before their turn, using their OPG in a bad outcome, or getting an XO where they do something awful, and then use their reveal power as a kicker. Short of this, however, the unrevealed cylon's power to sabotage the humans in most other ways have been fairly pathetic. The ability of the humans to catch cylons being secretly sabotaging is very high - and unless the cylon has the next turn and can escape, they often get brigged or airlocked or Cally shoots them, etc. While there have been some great games where unrevealed cylons kept the humans paranoid, fighting one another, wasting time, it's never been clear if any of this outweighed what they might have been doing as revealed cylons - which, with the Pegasus expansion cylon locations, is generally spending 2-5 turns doing nothing but collecting super crisis cards and then going crazy with them. The latter is not fun for anyone, but it seems more damaging than staying hidden and often having to keep helping the humans in order to stay maximally hidden (nothing I hate more than as an unrevealed cylon realizing that the positive skill card I felt I should play to stay hidden helped us overcome a crisis). In the core game, an unrevealed cylon who got found out and brigged could even be more effective by being able to openly sabotage as many crises (with one card) and space battles (with die roll modifications) as possible, but with the Pegasus Airlock, the human players are not going to hold back from simply killing off the stubborn unrevealed cylon who refuses to come clean when it's obvious what they are.
So, in general, what should stop a cylon who, from the start of the game knows they are a cylon, from revealing themselves almost immediately, and on their own terms? Why not just go get as many super crisis cards as possible (or whatever it is you think works best)?
I mean, other than it makes the game much less fun?