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.
I had significant problems with the way this was executed. Especially when they started talking about "bajoran faith" or faith in general.
When your "gods" are scientifically proven to exist then it has nothing
to do with faith. So when Kira says things like "You can't understand faith unless you have it" it rang really hollow to me.
I didn't like how the show seemed to almost pat itself on the back for depicting faith as an positive thing, but all the while it had nothing to do with actual faith. It seemed ridiculous that starfleet officers would continually take the attitude that the bajoran faith stuff was untrustworthy or hard to believe, when they themselves recognized the existence of the wormhole aliens and their ability to manipulate time/space.. There's nothing to have faith in there, it's all right there in front of them.
It's hard to really put into words what I'm trying to say, because I'm not very eloquent, but does anyone know what I mean?