This is my favourite Star Trek series and there's not much I would change. I really enjoyed the premise and the way it was set out.
I would keep the original characters, and keep them in their positions. Quark and O'Brien would have less featured episodes, Quark works well as a side character and O'Brien is boring as batshit. I would have Kaiko feature instead, it would have been a cool way to look at the plant-life. There could have been evil plants taking over the station and Kaiko using her botany powers to stop them but noooooo we have to listen to her husband drone on about not trusting Cardassians, like it makes him special (I mean, I like O'Brien well enough, it's not his fault he's the least interesting one, someone has to be.)
Sisko and Jake worked well, I don't think I'd change a thing. I think Sisko was incredibly well-written, he worked as being not-a-model-officer and his backstory was intricate in a way that made him feel more real. I didn't haye Wesley Crusher from TNG, but Jake was preferable. He acted more like a regular teenager and had an amazing relationship with his father and the senior officers (where as Beverley and the others didn't with Wes.) Also, Jake was never around long enough to feel annoying.
Major Kira was brilliant, I wouldn't change a thing.
Oh, Odo, I would change the whole Odo/Kira thing, that was weird.
I think tbey could have drawn out Odo's backstory a little more, build the tension and given us more Odo-centric episodes. The mystery was revealed a little too quickly for my liking.
Jadzia Dax - I love her/him/them. I know it was the 90's and most people weren't cool with genderbending or exploration of sexual orientation but holy shit Dax is clearly a non-binary pansexual, obviously they are attracted to all genders, if Dax was written today they could have a lot more fun with it.
Also, Bashir should also have been pansexual. Whoever wrote this series was a pussy, make these god damn characters gay. Julian was clearly f**king Garrek the entire time. It doesn't make any sense for him to be a hettie in the 24th century, he'll clearly get down with fellas, ladies, androgynous aliens, he's just so gay, anyone could see that he is GAY. Am I the only one? Am I going crazy? Can someone please acknowledge that both Jadzia and Julian were fully open to any kind of relationship, it's so obvious! I'm only saying this because I have the hots for Bashir, but that doesn't invalidate my point, he likes men too.
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Anyway,
I wanted to see more of Bajor. The citizens of Bajor were only ever what the writers needed them to be. They went from being peaceful, to an angry mob, to highly devout, to racist against all non-Bajorans. And it was always spoken as if their problems were global, their thoughts and feelings were global, as if they all went from being one thing to the next. It frustrated me. I think we should have seen more of Bajor and its people.