#4 Grouping
Too often, too many MMOs rely on people knowing each other outside of the game, either through real-life relationships, or maybe long-standing guilds. The tools that they put together in-game tend to be clunky and difficult to use. They are also very rarely, if at all, referenced in tutorial play, leaving many players to shy away from a system they don't understand how to use.
Grouping should be easy and encouraged in any MMO, even if it isn't necessary. At their hearts, MMOs are social games and developers need to be doing more to foster that feeling from within their worlds. I'm not talking about forced grouping, that kind of heavy-handed action shouldn't be necessary. If developers spent more time thinking of ways to bring players together, more players would probably start to group up.
#3 Housing
This one is fairly simple. The new MMOs released recently that actually include player housing have been few and far between, making it easily one of the most frustratingly ignored features in all of MMOs.
If you want people to feel as though they are a part of a world, and to create an attachment to it that will result, in the end, in longer customer loyalty and an overall better virtual world experience, then you really need to give them their own small part of it.
#2 Economy
One of the most important aspects of a virtual world is a living, breathing, interactive economy. It gives players something to strive for, it gives them a reason to work together, it gives them a reason to talk to one another. It serves a lot of purposes.
Too often now, developers don't pay enough attention to their own economies, letting them become (or designing them to be) very homogenized and dull, with little room for player interaction.
The power of a thriving economy and its value to a virtual world can't really be argued when one looks at the fact that EVE Online, arguably the most successful sandbox virtual world on the market today, runs a game with a thriving economy at its core. In that case, it's the economy that keeps players motivated and coming back for more.
#1 Strictly Social
Finally, the most mind-bogglingly ignored and underused features in MMOs today are those features that are purely social. Maybe it's finishing, maybe it's musical, maybe it some kind of relationship system but whatever it is, it doesn't have any practical value to the principal "goal" of players looking to play the game and level up. In terms of the flow of the game as a mechanical thing that has a beginning, a middle and an end, they are useless features. As a result, they often get buried under things that "have to get done" before launch and then post-launch fall victim to the number of things that have to be changed and improved from the original version. In short, looking at the score of development, they just don't seem to ever carry a very high priority.
This, I think, is indicative of development cycles that lose sight of the overall goal of MMORPGs to be virtual worlds that people inhabit and not simply games that people play. In order to create the feeling of a virtual world, time needs to be paid to the things that exist in the world that don't involve killing things or people and making XP and loot. There has to be something else and as long as new MMOs keep launching and ignoring their worlds in favour of their systems player are going to keep leaving in droves once the current crop of content is complete. They have no other reason to stay.