As a big DS9 fan, I agree with alot of what you've said. The religious aspects do seem nonsense alot of the time. It's so weird nobody on Bajor seems to care that their gods were actually found to be aliens that you can just go talk to. They just decided, well ok, but they're gods to us. The creators wanted to make a point about religion being real if you want it to be but I think by creating those circumstances if anything it shows how silly that is. They did at least try to balance it out by making a fundamental religious hypocrite as one of the main bad guys. I can't stand her though. And I know you're supposed to hate her but that's what I hate. She's so one dimensional. She makes her appearance by trying to assassinate someone purely for power and they're still trying to befriend her seasons later. Which makes it totally boring when she switches sides at the end. It's just like yeah, duh, finally. And since she's such a predictable, one dimensional bad guy she doesn't work well as a symbol for religion's faults. The pah wraiths also just sucked. I dunno what they represented or what purpose they had in the story other than to give some crazy energy battle final fire fight climax.

And it seems to me they tried way to hard to be dark sometimes. Things like Sisko himself poisoning planets and just one day setting up a conspiracy to bring the romulans into the war. And maybe the worst thing is coming up with section 31. I can accept if they want to show they when times are tough you are never really over the dark parts of human nature, but to add section 31 and say that since the beginning of everything they were there doing dirty stuff in the dark is just so contrary to the whole vision of tos and tng. It cheapens everything.

I did like the idea of the the war and the building up to the war as the main story of the series, but it does get tedious sometimes. Especially with all the shuffling around they did. Klingons attacking cardassia, now they're attacking us, now we're friends, now cardassia is friends with the dominion, now we're friends with the romulans, now we're not, now the breen show up, blah blah.

I don't think of star trek as being one thing. Every series is it's own world. TOS definitely feels unique. It was a lot more "sci-fi/fantasy" for one.