Hancock comes to mind. It started out as a comedy(?) about a bad-tempered superhero who's always screwing up and causing collateral damage, and then halfway through the movie it veers off into... a tragic love story with angels or immortals or something? I don't quite recall the details, but it was definitely not what the trailers had advertised. It was... odd.
I liked that show despite its flaws. And it definitely does have them. Like you say, they were more or less making each season up as they went; plot elements and characters from earlier seasons sometimes got shunted off to the side, the writing varied in quality (though that's true of every TV show), some characters kept reliving the same arc over and over, and the Cylons totally didn't have a plan.
I think it helped that I watched the show well after it aired; I'd already heard all the complaints about how the show started out great and went downhill at the epilogue/final episode/last season/middle of the third season/right after the pilot. (Okay, maybe I'm exaggerating about that last one, but not the rest.) So I was pleasantly surprised to find myself enjoying it, more or less, all the way to the end. I sort of liked the blend of hard sci-fi and weird mysticism, though I know the latter bothers a lot of people. The finale had some plot holes and some off moments, but also some excellent scenes, so it averaged out to a pretty decent capstone in my mind.
And I'd basically accepted that there wasn't going to be a brilliant ending twist. They'd built up all these unanswered questions, and there was no way the answers was going to be as interesting as the mystery had been. (I haven't seen Lost, but from what I hear it suffered from the same issue.)
See, this is why I'm really glad they stopped focusing on the space dogfights: they got old quickly. I liked that they started delving into the day-to-day life and concerns of the refugee fleet: supply and logistics, civil rights and unrest, and of course dealing with all the issues you get when you stuff a bunch of traumatized people into tiny metal boxes drifting through space and force them to live like that for years on end while their race is slowly hunted to extinction.
It's not to everyone's taste, I'll grant you, but if all you want is cool CGI space battles there are plenty of movies and shows that do this, and not very many that take BSG's particular approach.