There are some points that I wish they would improve upon... spending a season and a half to create a particular situation (that being two battlestars, people colonizing a planet, and the occupation by the cylons), then spending the next season undoing all of the developments that occurred in that past season and a half (destroying the Pegasus, rescuing people from New Caprica, the relationships that happened on NC falling apart, etc) for what amounts to killing off the Colonel's wife just feels tough to swallow. Why didn't they just keep the Pegasus and its crew around? The conflicts with the Admiral could have gone on for at least half of the season, instead of 2 or 3 episodes. Then they kill off the next two captains of Pegasus in one episode each just to put Lee in command for 5 more, after which he's back to KAG again. It makes you go WTF sometimes.
Its also hard to recover from giving people the best moment of a season within the first two episodes ("the maneuver" being this season's definite mind-blowing moment).