Because they're supposed to model superhero comics, which the devs, honestly, don't seem to read.
Think of how important secret identities are for Spider-Man, Superman, Batman, et al. There should be contacts you can only interact with in your secret identity -- either because they won't talk to you (J. Jonah Jameson), or because you'd put them in danger in your superhero guise (Mary Jane Watson), or other reasons. Likewise, you should be required to switch out of your uniform to infiltrate some areas -- no one will let Batman into their shady factory, but Bruce Wayne, who says he wants to buy the place, will be given the keys if he asks. Criminals should also be less likely to start mischief in the presence of a costumed hero, especially after a level or two.
I just got through playing Assassin's Creed Brotherhood. In a lot of ways, the protagonist is like a renaissance-era superhero, with a variety of wondeful toys designed by Leonardo Davinci, an acrobatic mastery of urban terrain, and combat moves that allow him to battle a dozen enemies at once.
I mention this because some missions actually require a low-profile mode, not unlike switching to and from a secret identity. In that spirit, I would love to see a superhero mission reminiscent of that classic situation where a hero has to switch from his secret ID to his costume, such as by creating a distraction using the environment. Tie that in as a mission sub-objective.
Hopefully, the Star Wars Old Republic MMO will shape up as a blueprint for how MMO's should evolve. It'll boast a mini RPG for the various types of characters it has to offer, complete with a supporting cast and cutscenes that develop relationships and build drama.
My strong suspicion is that CoX was a superhero game because the developers wanted to make an MMO and seized on comics because it was unclaimed territory, not because they had great knowledge of or passion for comic books. (And yes, I know Statesman claimed he did, but his game sure doesn't show any evidence of it.)
I don't like "healer" superheroes either. It's very much not part of the genre. Even a powerful white magician like Dr. Strange can't do much for a friend who's been beaten to a pulp. Raven from the Teen Titans is as close as I've seen to a healer hero, and for her the act of healing is both dicey and strenuous. So, IMO, it's trying to fit a square peg in a round hole.
Having said that, Jack Emmert was the guiding hand behind CoX, and he's a passionate comic book fan. He had lots of great, innovative ideas, but like so many MMO's that spent years on the design table with the ambition of redifining the genre, they wound up at a point where they realized that they were biting off more than they could chew. Without a big license, it's unrealistic to expect to pull in huge audiences by being radically different from established expectations. Rather, there's a greater likelyhood of alienating potential players through lack of accustomed features. Some people like playing healers, and others feel combat is missing some integral component without them.
People are funny. They want something that's different and engrossing, but they also want something familiar and facile. By way of example, even in 2011, DCUO is taking heat for not having a crafting system. Because regardless of genre, every MMO should have merchants and auction houses, right? And a factor that's at least as important a consideration as the player base is the capital base. Investors tend to favor proven formulas over taking risks, and aren't shy about asserting their lack of artistic pretensions.