A couple of things
1. The TNG crew crossing over with the DS9 crew. Even if it was for just a two parter would've been cool.
2. Bring back Capt Jellico! Our resident Cardassian expert was given command of the flagship the last time there was to be a war with the Carddies but in the Dominion Arc we see neither hide nor hair of him.
3. Bring back Capt Maxwell from TNG the Wounded. After doing "hard time" in those Federation penal resorts they send criminals to in this era. It be awesome to see such a captain given a ship to fight the Cardassians again.
4. A more in your face dealing with Section 31, Starfleet Command and the Federation council. With the bent actions and support for those actions by these 3 groups in INS and DS9 "The Dogs Of War". Concerning the sanctioning of the use of the morphogenic virus and the Council voting to withhold the vaccine, and the removal of the Ba'ku from their home planet. I'd love to see Sisko or Picard confront them over how the government is being run. Sisko seemed to complacent given his own guilt from "In the Pale Moonlight". Bashir tried to confront Adm Ross but was struck down. Picard could be more forceful in the confrontation with the Section, Command or Council.
With what we've seen most recently in STID with Adm Marcus and the Enterprise, and you think about Adm Carthwright setting up the Ent-A in TUC and Adm Doughtery willing to throw the Ent-E under the bus for the particles in INS. Is the Federation government and Starfleet so bent that they don't care about sacrificing the flagship of the fleet because it doesn't line up with the agenda the Fed is pushing at the moment?