Ron Moore was wrong. He kept saying that the BSG finale wouldn't be what anyone was expecting, but my two main predictions came true. I won't bother with a detailed review (there are plenty of those to choose from) but here are a few random thoughts:
Earth: The Colonials wore suits and ties like us. They worshiped Greek gods. Well before "All Along The Watchtower" it was inevitable that their world and ours would be connected somehow, and since a major part of the show's premise was the quest for Earth, I always believed that the fleet would eventually land on Earth, and it would be revealed that all this happened thousands of years in the past and the Colonials are our ancestors.
Starbuck and the Head People: Ron Moore and co. were in a lose-lose situation with this one. No matter how they handled the mystery of what the resurrected Starbuck, Head Six, and Head Baltar ultimately were, there was no way to please everyone. From the many Internet comments I've read, I think people were upset that we didn't get some kind of Star Trek explanation, especially in Starbuck's case. The term "Star Trek explanation" refers to TNG-era Trek's propensity to reduce any seemingly unexplainable phenomonon to a quantifiable, not-at-all-mysterious thing, usually by way of dense, technobabble-heavy exposition. All in all, I'm not unsatisfied by the choices Ron and co. made here.
The Flashbacks: Watching the flasbacks during Daybreak's first hour, I assumed that they would pay off during the story's final two hours, that the character's actions in the flasback sequences would somehow inform their choices in the present day. Mostly, I was wrong. Except for the Baltar story, which set up his eventual choice to become a farmer like his father, the flashbacks just felt like a late addition. I mean, did we really need to see a drunken Adama vomiting in an alley? And yes, I understood that the pigeon in Lee's apartment was supposed to represent Starbuck, but that, too, seemed tacked on. In one of this interviews about the finale, Ron Moore revealed that it was originally concieved as a two-hour episode, but then the network gave them an extra hour fairly late in the game. More than anything else, the flashbacks look like an attempt to spend the extra hour they'd unexpectedly been given.
I haven't seen every episode of BSG, some of it is just too dark for my tastes. However, I think that Ron Moore and the writing staff did the best job anyone could have done in telling the story of Battlestar Galactica. To do four seasons of a science fiction TV series and never once fall back on genre conventions like time travel, evil twins, ray guns, bumpy-headed aliens, and cardboard characters is a feat that's never been accomplished. It's a testament to the good that can come when you scrap an old and tired way of doing things in favor of a fresh approach.