This list might be expanded in the future if I encounter a suggestion worth mentioning.
1. Merge Enchanting rods - now only the better rod is required to enchant an item with lower level enchant.
2. Merge Zul'Gurub Bijous and Coins - instead of 9 different versions of Bijous and coins, there is only Hakkari Bijou and Hakkari Coin now. This will help with bag space and make it easier to search them on Auction House.
3. 1 hour Paladin buffs - 30 minutes small version, 1 hour the greater one.
4. Better item stacking - a few items still need a stacking update, for example ores should stack to 20. It's also worth looking at Soul Shards and Ammo, but that's optional.
5. More bank slots if technologically possible. You did it with quest log, maybe you can do the same with bank slots?
6. New flight paths, especiall for Alliance in Kalimdor. Tauren druid flight path in Moonglade to Thunder Bluff needs to be shortened or maybe even replaced with some kind of teleport. Add connection between Grim Reaches and Kargath. Try to shorten Hyjal flight, this one always takes way too much time.
7. Improve pet experience gain - It takes forever to level a new pet as a hunter.
Leave more suggestions below so this list is more complete.