I have a few:
--I would have made T2 pants obtainable without MC
--I would've made acquiring Thunderfury more like acquiring Atiesh
--I'd add a flight point to Rebel Camp
--I'd add a repair closer to Stratholme than Chillwind Camp (although eventually they did do this)
--One of the top ones is that I never understood why Blizzard didn't try to get metro areas all on the same servers. Nothing sucked more than meeting a new friend IRL but not being on their server.
But I'll tell you one thing: I would specifically never touch Duskwood, Blackrock Depths, or Stratholme, some of my favorite places in the game.