The absurdly-limited amount of personal-appearance customization, even within the "you look like your gear" MMO standard.
I suspect that I'm going to be comparing games to City of Heroes and finding them lacking for a long time to come...
That's sort of something I hold against many games, and I don't just mean video games in this regard. Style should not dictate substance, and yet in
so many game systems it does. SW:TOR does better in that regard than most, in that some blaster types can heal, and some cloth-y types can tank, but it is still the case that how you want to play determines how you look and what you wield.
This is something that Champions Online is actually slightly better than CoH with regards to in that there exists in CO the fabled "ranged tank," who can look like pretty much anything you want, and can utilize any of some 60 powers to be a good tank. (OK, yes, your slotted passive needs to be one of three things. You're limited in that. But that's mostly it. It's also highly recommended that your primary Super Stat be Constitution, but even that is somewhat negotiable if you're willing to be a pseudo-tank for the first 20 levels of your life.)
It's something that Dungeons and Dragons is
horrible at. If you want to be a tanking type in D&D3.5, you either have to play a Crusader from the Tome of Battle, you have to be a Cleric, or you get to suck at your role and pray your GM plays his monsters as stupid. If you want to play a sword-and-board character, you
will be a tank, and if you're not a Crusader you're still going to suck at it. If you want to play a Cleric who wears cloth, instead of chainmail, you are degrees more vulnerable than if you just wore the armor, with no effective benefit for wearing cloth. If you want to wield a bludgeoning weapon, you will deal less damage on average than if you wielded a similar piercing or slashing weapon. Et cetera.
Honestly, the best game at letting you be whatever the hell you wanted and still function however the hell you wanted to function was Mutants and Masterminds, which no one in their right mind would ever be able to translate into a video game. But it's great at that; if you want to be a shapeshifter whose powers change with your form, you can do that. If you want to be a hero made of electricity who contributes to party efforts by gathering information and making everyone else super fast or teleporting heroes around the city, you can do that. If you want to be an inventor who has no intrinsic powers but can jury rig whatever device the team needs in 30 seconds, you can do that. If you want to play a teenage kid whose psychic powers make him capable of lifting cars and shrugging off bullets, you can do that. If you want to play a US Army General who, due to a weapons project gone wrong, no longer has corporeal form, you can do that. And all of these things will be useful to the party. (And if your GM's good, everyone will feel like
they're the MVP.)