I think that the religious plotlines were generally better when dealt with realistically.
Basically, the struggle between whether or not science or religious dogma belongs in schools, the political manouvrings in the vedek assembly: Good.
Anything to do with the pah-wraiths and the Bajoran apocalypse: Not so good. They completely botched not just one but two great villains - Dukat and Winn - in that arc. Also it sucked.
It's a shame, not that they passed around their political material in later years to non-Bajoran arcs, but that what the Bajorans were left with wasn't any good.