Wow, long thread, so these may have been mentioned already...
- Allow thieves the tabletop utility of picking locks and disarming traps. This was one of the most exciting aspects of DDO, a pleasant departure from thievs/rogues in other games being "stabby stabby" all the time.
- Randomly generated dungeons, similar to what was introduced in EQ's Dungeons of Norrath expansion. End game content consisting of running the exact same handful dungeons over and over with the exact same monsters placed in the exact same locations is, well, boring.
- Some kind of system in place to limit the constant jumping around common in pretty much every MMO today. In PvP especially, if you are constantly hopping up and down, you should take some kind of hit - be it accuracy or stamina or something.