Here goes a few things that i would like to see in a "perfect" MMO.
1. No set factions, i would want to be-able to pick and choose sides as i please.
2. A giant game world (i'm talking 10 the land mass of Azeroth + outlands combined) with extensive underground tunnels & dungeons
3. No instanced places so no matter where you go you can still be killed by another player.
4. The ability to build and control towns, and also the ability to destroy them with siege weapons/magic/other means
5. Smart AI. eg A local encampment of lizardmen(or anything else) has been left undisturbed for x many days and has built up sufficient force to stage a raid on a village in the area
5A. Unique "boss" monsters that are effectively world raids. They would evolve from normal NPC's if that NPC has stayed alive for a certain number of days/weeks. If applicable these could also join in a raid on a local village
6. Ability to loot other players gold when you kill them (possibly even weapons/armor as well)
7. "secret" and/or out of the way places that people only know about if they find it themselves. Unfortunately this probably wouldn't happen because we all know humans like to go blabbing about these kind of things to anyone and everyone