I'd replace the current throne room in Org with a giant bank. This way i could park my character on top of the bank and look down on org like I used to. The throne room could go back by where the brawler's guild is, or we could use Garrosh's throne room.
If alliance is stuck with Stormwind, I'd like:
-the dock and the canal to be on the same level
-the canals to be made larger to accommodate ships
-house boat vendors that change from time to time
-a large active military presence in the barracks, also larger barracks
-more random encounters, quests, mobs in the city
-taller and more complete buildings
blah, new sig... something something
I'd relocate all of the stormwind stuffs to stromgarde and add a boat from there to Kul'tiras which lets you have your own boat... pliss blizz ;_;
Add proper npcs to all of them to make them on-level with each other.
Make Echo Isles a proper city. There's no point in giving trolls back their own faction area if it's defunct at level 5...
Restore Silvermoon a bit visually. I don't want them to waste time giving us flying and all this fancy crap, but get rid of wreckage and reconstruction and add a new wing or two with buildings for some of the trainers and vendors who are currently just standing on sides of roads and such. They could also throw transmog and reforge in there.
It honestly really annoys me that after all this time, they stubbornly and pointlessly refuse to add some extra NPCs in each city so that we don't have to be forced into shrine and orgrimmar.