First, I will say there will never be a perfect MMO, and what I like will not be for everyone. Second what I would like does change between genre's, so a fantasy MMO has different needs then a space travel one. For my list I will go with fantasy.
Being able to spec your Character in more ways. Sure your warrior is a tank, but if the tank role is filled they should be able to assist the healer by handing out potions and poultices, or the use of traps to increase their damage and control the battle. The ability to do stuff when they are not being taking a beating while protecting the group. The same thing for other AT's. there should be enough overlap that they can help fill in other roles, especially if other classes are not available.
Interactive environments. There should be traps in the dungeons that require a dungeon crawler type player to avoid, and they need to be random. It doesn't work if they are in the same spot every time, and a person with no detection skill tells the group where everything is. . That doesn't mean I want a thief in every party, but the ability for any player to spec to those skills. The same with crafting skills. They should have an effect in certain situations, it may just be the miner sees a rock formation they can knock down so they can cross a chasym instead of going around speeding things up, or the jeweler noticing the ring you think is the quest item is fake, so you search further for the right ring.
Better AI. The AI should set sentries and ambushes for you. Your invading their home, they should have advantages at times. Not something that wipes out a prepared group, but still a risk if you get caught of guard. The AI should also go/call for help if there are allies near by. Why would you let 4 guys beat on you, and you not try and get your friends that are right around the corner. Also if there all multiple factions, then your groups factions should come to play. You sneak up you should be able to watch them fight it out, and then pick off the winner. If you have good faction they should help you fight, bad they gang up on you, and if neutral they should cheer you on or go their own way.
Tons of gear. There should be plenty of gear, enough that 100 players in a room will not look the same. You should also be able to add to them, dye, runes, and other skills to improve or change effects.
Powers should level with you. It is time to learn a new version instead of going to a store or just learning it, you quest/train to improve. So your tangling vines, instead of just a root, you can choose between thickening the vines for a longer duration or adding thorns for a DoT effect. Next time you can add poisons to the thorns for different effects, or if you chose to thicken the vines you can make them a creeper that limits the targets actions by entangling their arms.
That is a start, though I doubt I would ever see a MMO like that.
Now I do agree on EQOA's openness, you should be able to go from one area to the next with no loading. If I am flying high above the mountains, why so a stop because of a few trees on a border, or why is the only way from one area to another is through these gates. Though open worlds do need a map. I remember back before they added group symbols to EQOA. We had to memorize the terrain, so we could give directions to the camp. Go due west till you reach Y shaped tree, now north to this rock, now go north west till a mountain range and follow it to the entrance. It is so much easier to coach here and follow the arrows.