Deep Space Nine is fabulous, but it needs a makeover because it is missing several important things:
*If at all possible, Quark's really should not be its own instance.
*Holosuites added to the top floor.
*Hologram of Morn, or Morn himself if his species is long lived, added to Quark's. Should be able to buy him a drink.
*Sitable stools added to Quark's.
*Darts mini-game added. Play with your friends, gain skill at the game the more you play, etc.
*Infirmary is missing! Doctor Bashir did not practice medicine by the Exchange! Give us Bashir's Infirmary.
*Tailor really should be Cardassian instead of Vulcan.
*Security Office is missing. Place Odo's bucket subtly in a corner as a tribute to the constable. Perhaps the new security chief (who should be in the bajoran militia uniform) can offer us officer training or something relating to ship's crews.
*OPS needs to allow us to walk into Sisko's old office. Put his baseball on the desk as a tribute to him.
*Runabouts, which are sold only at DS9, need to be given some kind of real in-game function. I hear the shuttle system is going to be cool. Are runabouts better than a standard shuttle? They should be.
Any other suggestions?
EDIT: added my one last thought "Instead of beaming onto the Promenade, we see a cut scene of the DS9 "pizza-slicer" doors opening, our Captain walking out all epic like, and then we are standing on the Promenade."
EDIT2: Morbius1's excellent ideas:
Like the OP said, open up the entrance to Quarks. PLEASE TAKE OUT THE STUPID RAMP. One way to save polygon load (so you can merge it to the rest of the promenade) is to add turbolifts like you had in Club 47 instead of that monstrous ramp. It might not be totally accurate, but it's better than that ramp.