The BSG ending was significantly better than the LOST ending. While BSG had a couple ongoing “mysteries” which were never adequately explained in the show (Starbuck, “they have a plan”), it was less a part of the show than the mysteries of LOST. Moreover, BSG had far more references to relevant mystical matters early in the show. At the very least, we had the example of Head Six.
I also think it’s very, very important that Baltar actively attempted to discover the nature of Head Six. He was curious. He came up with hypotheses and tested them. This is how you’d expect someone who is smarter than celery to act. The LOSTies never did squat. Showing us a character trying to figure out the nature of Head Six and failing to find a (relatively) mundane explanation is a great setup for revealing her to not have a mundane explanation.
The problems I had with the BSG finale were
(1) the unnecessary, cheesy robot montage at the very end,
(2) the cheat with Earth not being Earth, but not-Earth turning out to be “Earth”
(3) the deliberate regression to neolithic technology (although this doesn’t bother me quite as much as it bothers some, it’s still a bit hard to swallow)
(4) the complete non-answer of the long-established mystery of Starbuck’s return
I think it’s safe to say we get an answer for what she is - the same thing as Head Six. But that’s only a partial answer. How did she get resurrected? Why did she get resurrected? Why did she show up exactly when she did?
I never thought LOST would have a strictly accurate scientific explanation. I did think, during the early episodes, that it might well have a “TV-science” explanation. Eventually I realized that wasn’t going to happen. Then I thought it might possibly have a science-fiction explanation. Eventually I gave up on that too.
But while I would have preferred a more realistic LOST, my problems with the finale (and really, the entire final season) are that we do not get answers for important, long-established mysteries. Also, some of the few answers we do get contradict earlier episodes, or are just plain bad.
I do prefer science fiction to fantasy, in general, but that’s a very general preference. It’s not the mysticism of the finales itself that bothered me.