Are you happy with the base game? If it's getting "routine" then an expansion is worth it.

Is it cost prohibitive? If not, take a shot. Worst case, you don't use it (maybe sell if for $10!)

I like a lot of things that go with Pegasus (new characters, new Cylon Fleet, more crisis), and it would be the natural next step. I t think it would add some variety but still offer similar play to your current games. (maybe?)

I have heard of people going straight to exodus - especially liking the "allies" in the game. I don't think I have ever played a 3 player Exodus, not sure I would.

The first thing that comes to mind is the fact that a few components won't be usable in three player games (for example, the mutineer and cylon leaders in Daybreak).

In general there's a lot of talk about which expansions make the game easier for one side or another, but I don't know that any of them have a particular effect on the balance for different numbers of players. Maybe the Cylon Fleet Board in Exodus would be harder with three? (edit: and the Ionian nebula would be less prone to the swingy player eliminations that make it so unpopular, but when they do happen they'll be pretty decisive) The execution mechanic (most prominent in Pegasus) might also have a bigger impact, but I think that might be a positive one (I actually don't have much experience with three players, but if you have a fair number of games in which the cylon convinces one human to brig the other and then takes over, the airlock might actually be a welcome alternative.)