There's not much I would've done differently with DS9. However....
1) Bring Bajor into the Federation at the conclusion of the series.
2) Make the Klingon-Federation War more devastating, or not even do it. I think DS9-except for Martok, Worf, and Kor-did a pretty lackluster job with the Klingons. They made them too weak and pathetic warriors. As much as I enjoyed "The Way of the Warrior" looking back on it now, the Klingons were terrible.
3) Make the Hunters part of the Dominion. I think it would've been cool to see them again, plus the Tosk aliens looked like Jem'Hadar to some extent so it might've explained their origins too.
4) Less Mirror Universe and Ferengi episodes.
5) Would've killed off Dax in "Change of Heart." After reading some of the other posts, I probably wouldn't have brought the character back. Or maybe as a man.
6) Better S31 episodes. The only show that did them justice was "Inter Arma Silent Leges".
7) Made the Tholians or Gorn the surprise member of the Dominion instead of the Breen. I thought the Breen were okay, but not enough of a real shock to me. Even though they had previously had as much or more screen time than the Tholians or Gorn, those TOS races would've excited the fans more IMO, esp. if the FX had been good.
Would've left Dukat trapped as a blind Bajoran. I think it would've been ironic and fitting for him to spend the rest of his life, or at least some part of it as perhaps a destitute beggar, living off the charity of the Bajorans.
9) Had the Pah Wraiths ally with the Dominion. They would've attacked the wormhole, allowing the Dominion to send ships in. I probably would've had Sisko ascend in the battle to stop this from happening inside the wormhole.
10) More Maquis cameos would've been cool. I think the Cal Hudson story deserved a follow up. So did Tom Riker. It also would've been great to see Ro as a guest star. I agree with some of the other posters that putting Chakotay, Seska, Torres, or Tuvok in one of the DS9 Maquis stories would've been great. I also think a Sisko/Janeway scene would've been cool in "Caretaker."
11) Made T'Rul a recurring character. I would've liked to have seen more of her.
1) Bring Bajor into the Federation at the conclusion of the series.
2) Make the Klingon-Federation War more devastating, or not even do it. I think DS9-except for Martok, Worf, and Kor-did a pretty lackluster job with the Klingons. They made them too weak and pathetic warriors. As much as I enjoyed "The Way of the Warrior" looking back on it now, the Klingons were terrible.
3) Make the Hunters part of the Dominion. I think it would've been cool to see them again, plus the Tosk aliens looked like Jem'Hadar to some extent so it might've explained their origins too.
4) Less Mirror Universe and Ferengi episodes.
5) Would've killed off Dax in "Change of Heart." After reading some of the other posts, I probably wouldn't have brought the character back. Or maybe as a man.
6) Better S31 episodes. The only show that did them justice was "Inter Arma Silent Leges".
7) Made the Tholians or Gorn the surprise member of the Dominion instead of the Breen. I thought the Breen were okay, but not enough of a real shock to me. Even though they had previously had as much or more screen time than the Tholians or Gorn, those TOS races would've excited the fans more IMO, esp. if the FX had been good.

9) Had the Pah Wraiths ally with the Dominion. They would've attacked the wormhole, allowing the Dominion to send ships in. I probably would've had Sisko ascend in the battle to stop this from happening inside the wormhole.
10) More Maquis cameos would've been cool. I think the Cal Hudson story deserved a follow up. So did Tom Riker. It also would've been great to see Ro as a guest star. I agree with some of the other posters that putting Chakotay, Seska, Torres, or Tuvok in one of the DS9 Maquis stories would've been great. I also think a Sisko/Janeway scene would've been cool in "Caretaker."
11) Made T'Rul a recurring character. I would've liked to have seen more of her.