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.
Couple it with a more true-to-comics faction based PvP system (heroes vs. villains) and going incognito would mean dodging PvP, as well as the NPC agents of your enemy (cops or organized crime).
No one should be required to use a secret identity -- the X-Men don't consistently do so, for instance -- but it's a core component of the most popular superhero characters in the world, and for MMOs to not support it at all makes me wonder what it is they think they're emulating. (Of course, this is the same industry that gave us a Star Wars MMO without the ability to fly a spaceship for several years and originally made it essentially impossible to be a Jedi, because everyone was wanting to play a moisture farmer or something.)
And this also goes for combat and healing -- every superhero team isn't loaded up with "healers" (there are probably fewer than a dozen who've ever been a part of the JLA or Avengers in their entire lifespans), but CoX requires them, because the developers are using EverQuest as their starting point and not, more logically, a console fighting game, where characters recover quickly from most wounds once they're out of combat. That would be much more true to the genre, be easier to balance (making healers appealing to play is a headache in all games) and have more appeal to non-MMO gamers, who are most of the theoretical gaming audience.
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.)
Hrrrm. I think a lot of your points are simply the difference between pen n paper games, and MMOs. I'm not sure how you would implent game mechanics to make secret identies mean something without making them a must have.
I know role players ingame will just use a different costume slot of RPing thier alter egos, but nothing mechanics wise supports it.
I'm not sure how much you've actually played though if you think healers are the norm. In my experience of playing, you rarely get 'healers', one of the things I most enjoy about heroes is there is no need for a tank/healer/dps trinity. Buffing, debuffing and control is the more common and generally more sought after than a character who has focused on getting healing powers. Just about everything can be done by a pick up team comprising on any mixture of characters - which is good and bad depending on what sort of game you're seeking.
PvP is pretty much the suck in heros. The systems are there for mixed zones where you can commit acts of carnage, there's bonus extra special rewards for doing so, or for doing missions in the PvP zones, but for most players, they hate the idea of being forced to combat.
Cities is also a mish mash of stuff, western and asian comic tropes, plus elements of steampunk and more.
There is some interesting stuff in the backstory, but most often you'll be teamed and missing the text. Of late too, the storyline is all focused way too much imo on the new expansion, and updates keep hammering the thick story plots at you.
But it tends to be either play with a RP group, or you just there to bash things in face a lot.
As said, the costume character is wonderful. What you wear doesnt effect powers, so your damage with standing hero can be in battle armour mech like, or a zombie bride.
There's a lot of variety between enemy mobs. The same old same old maps get annoying after six months. Each side (hero/blue, Villian/red, and prateoria/gold) all were added at dofferent times, and have quite different stry arcs. Your now forced to try goldside with your first character, but I think you are better off trying red or blue asap. I'd make the character and then make another for each side. Heroes supports a lot of characters - 12 server with 8 character slots each.
http://wiki.cohtitan.com/ has a lot of info about the game if you want to see what the enemiy groups, missions, story lines are like.
But trials to all 3 are probably free - so I'd just give them a try.