I disagree that the "religious stuff" was mumbo-jumbo. I sort of don't mind religion when the gods are demonstrably real. And the really interesting aspect of the religious storyline was the intersection with Bajoran politics. I felt that the non-linear nature of the Prophets' existence fully justified and explained the pseudo-mystical nature of the prophecies, the "Emissary" plot line, etc.
Also we got a whole lot less of "blue team hates red team on planet of the week, away team in peril" bullshit, and a lot more fleshed out recurring characters.