WoW was both a blessing and a curse. The single clever thing WoW did was take all the good bits from other MMOs and put a large amount of shine and polish on them. I'm still at a loss to explain so large a success though. It has however made it much harder for any other MMO to be "different".
The biggest problem I have with MMOs (And remember this is all from my perspective. Another player will have different needs) is levels and the associated grind that goes with that. Every dev team and publisher seems utterly focused on churning out what is pretty much a guided tour of their game. "I'm level 43. Now I go to this area to play". It's a fundamentally broken and redundant mechanic for many reasons. Not least of which is penalises people with less gaming time than the zoned rats who dominate these games today. It also means you have to spend a lot of time developing a path through your game that you expect the players to take rather than creating a world. Levels are imo the single worst thing in MMOs today. They do more to promote static and unchanging player experiences than anything else.
Let's look at two games you'd think were like chalk and cheese but are actually very similar. Ultima Online and Eve Online. Ultima Online was the first big graphic MMO. Eve is a more modern Elite style MMO. I'll describe each one in turn.
1. Ultima Online.
UO has changed a lot over the years but the fundamentals are the same. It's a classless and leveless fantasy MMO. Skills are trained through repeated use and almost the entire game world is open to play from the beginning if you're nimble enough to get somewhere. Occupations are varied. Many characters in the game have vocations other than combat and many have never fought a battle at all. UO has many problems but it also gets many things right.
2. Eve Online. Eve is a classless and levelless space MMO. Skills are trained in realtime. You set a skill training and a certain amount of time later it becomes trained. This even continues when the player is offline promoting a constant sense of progress. Eve like UO is an open ended sandbox. No levels means no need for a strict progression through the game and most importantly no need for an "endgame". Players in Eve can be miners, pirates, industrialists, company managers or anything they damn well want. Eve however is probably the most hardcore PVP game currently on the market. Nowhere except for docked at a station is safe. Players can be killed anytime and anywhere (Although in certain circumstances there are consequences for doing this). This combined with the many ingame ways to "be a bastard" makes Eve a very hostile and unfriendly game. Obviously there's a sizable playerbase who likes this but I do wonder how many players would leave if a PVE alternative came along.
One other thing I wish to talk about is the second biggest problem MMOs can have (Although to be fair this is not as bad as it used to be). Putting PVP and PVE players in the same environment. It just doesn't work. Apart from the two sides of the player base being utterly hostile to each other's playstyles (Disclaimer. I hate PVP in almost any form) it adds extra burden to the poor dev team trying to keep the game "balanced". What works for PVP doesn't always work for PVE and vice versa. For me the best thing any MMO can do is segregate the two side totally.