I still think that, despite the show's quality, Deep Space 9 did more to damage the franchise than anything Nu-Trek ever has. It introduced so much shit that allowed this more actiony, dramatic Trek incarnation to occur. The show itself was good, but holy fuck I wish they had never introduced things like the Dominion War, Section 31, Star Fleet Intelligence, the Marquis... just... ugh.
Edit: I just wish Star Trek had stayed in its niche of optimistic space exploration instead of the militarized... garbage its become.