- Starbuck shouldn't have been an Angel (they thought of that at the last minute; if they wanted to do that - lets face it other scifi shows have, Daniel Jackson style - they should have set it up far better).
- Particularly, the entire "Final Five Cylons can be anyone" concept, breaking their past rules, was a massive character assassination of Tigh, Tyrol, and Anders (I may, may have accepted one, not all three). This should never have been done.
- Making "Earth" the dead colony of the Thirteenth Tribe...who were actually Kobol's Cylons, was a great idea; it meshed with the core mythos of the show. I'd keep that.
- The writers themselves would admit that they lost complete track of Apollo and Roslin in season 3, though admittedly they fixed them up surprisingly well in season 4. But even Ron admitted that Apollo/Dualla was a mistake...it's just that instead of ending it, they tried desperately to salvage it for 30 episodes, long after they should have cut their losses.
- I don't blame Ron for the network forcing him to make season 3 a season of bottle-episodes and drop the Sagittaron Storyarc -- I blame Ron for not being transparent with fans about just how much this was affecting the show at the time. It was Farscape season 4 all over again.
So "Starbuck as an Angel was poorly set up" (and probably should never have been done), "Head-Characters are angels, not chips" was poorly done and should have been better set up (their behavior is contradictory at times), and the Final Five should not have been done. Well, making the Final Five the "hidden Imperious Leader" of sorts would have been okay, which is sort of what they did, but the choice of Final Five was for shock value. That, and the Cylon Plan should have been "track humans to Earth to destroy it". Those are the big issues much of the rest stems from.
I'd argue that having Tigh revealed to be a Cylon actually made him a better character. It lead to him deciding to become a better person instead of the drunk he usually was. It was great development and I wouldn't get rid of it because a small minority don't like it.
Also the less connection to the original, the better. So no Imperial Leaders, cowboy planets or other random stupid crap from the 70s. I'm sure they could have made a three faced disco alien work, but we're better off without it.