I think with franchises being so important in movies these days, a trilogy is almost guaranteed (assuming the presumptive first movie performs well, of course). And I would lay it out exactly how you described: the first movie depicts the holocaust and Galactica pulling together a ragtag fleet of survivors. Maybe there'll be some big battle at the end to give the audience an emotional lift and end things on a hopeful note. The Pegasus story would be perfect for a middle chapter. And then the fleet finds Earth in the third film (I wouldn't be surprised if there was some sort of epic 'battle for the fate of humanity' where they have to defend their new world, or something).If not that, then trilogies are all the rage, in which case the first film can be about the initial attack and the ragtag fleet's escape, with hints that the Cylons are still in pursuit. Second film would probably be a great opportunity to tell the Pegasus story, which is really one of the best stories in the BSG mythos. Third movie can be the quest for Earth.
To be honest, just thinking about the possibilities has gotten me excited. A three-movie story could be great, if executed properly.