Well... Character customization... I didn't check City of Heroes, but what you say reminds me Project Entropia (now Entropia Universe). You could alter your nose shape, size, placement; eye color, placement, and "rotation", and some more. Tho' there you started up with basic orange jumpers, but.. hmm... Well, it's a pretty different kind of game
Quest.. as a NPC hater, I hate quests given by NPCs also
Probably because of their dullness, and that these quests are for masses. Well, you mention that they're a good way to get into the world for new players. Well, I bet they're, but at least for me they're too easy, and a bit too unnatural. Dunno how I can explain it, but I've always preferred asking people about directions to a city (Wurm) or running thro' teleporters (Entropia) for my own bussines, than doing a quest of some sort... Played Linage II for awhile, but, damn, I've deleted it after 20 minutes because of these hack'n'slash thingy.
Skill system... Well, I should mention here Wurm and Entropia again
While Entropia's skill system has very little affect to gameplay, then Wurm's... Wurm's skill system is somehow good, but now kind of unbalanced. And also, that this is alpha like version, bugs happen, and then some people can grind skills fast. One thing to mention here - skill gaining shouldn't be a priority for a player, nor the gear race. One thing I hate about Wurm is that, after the stand alone noob days, you usually play to get your skills higher, or to build or create something "uber". Example ? My friend: "Look, this guy has 70 digging skills and has a shovel of 60 quality level affected with Wind of Ages and Circle of Cunning!". And worse, what he says is mostly like this.
Equipment. Very important in Project Entropia, in Wurm important as skills. Well, in Wurm, skills are important, but the items you use should have same quality level as your skill level for best effect. You can however achive more with good skills and bad equipment than with bad skills and good equipment. IMO it's kind of balanced there... kind of.
That would be my opinion now
Anyway... for me now, after the Wurm, these aren't the "most pleasing" features for me. There are just good combinations, not stand alones. Wurm is a great example - good concpets, some niice features, but the game mechanics are terrible, based on right clicking, resulting in a game fun for newcomers, unfun for those who can't stand doing one thing for some time.
Anyway, I'd like to mention that I've never found one type of fun from MMORPGs. Fun like that is in pen and paper RPGs, but it's not from playing your character... Rather like sensing the teamwork, also fun from doing something, hm, not fitting in human's mind ? Some kind of quest like fun ? Not that kind of quest that is done by masses, that doesn't affect the real world... well, something like that :/ Dunno how can i describe it.
Wha-- ?...