What's ironic about BSG is that the show was telling us all along that there was supernatural stuff happening -- prophecies that came true, talk of destiny, mysterious figures that called themselves angels of God -- but the viewers (myself included) didn't believe it and tried to rationalize it as having some secular explanation, because we weren't used seeing magical realism in the context of space opera. So when the finale confirmed that all the mystical and supernatural things were actually true, many people thought it was a retcon, even though the show had literally been telling us all along that these things were supernatural. For my part, my reaction was "Ohhhh! I've been looking at it all wrong, it actually makes so much more sense if it was never supposed to be rationally explainable in the first place."
I don't think the same goes for Lost, though. I gave up on it after a couple of seasons, but from what I've read about it, I think there was a lot of readjustment of the story plans as writing staffers came and went.