I'll preface my .02 inf with the caveat that City of Heroes was the first MMO I ever played, and as such is the benchmark against which I compare all other MMOs.
That said...
1. Quality of Writing: CO's combination of pun-based humor, over the top mannerisms, and thinly veiled pop-culture references doomed any chances I ever had of taking that game seriously. The intro arc in Westside even includes some good old fashioned racism with Hi-Pan (get it? like Lo Pan from Big Trouble in Little China, but SO DIFFERENT) and his inability to pronounce the letter 'L'. Get all the way out of my face with that crap.
2. Teaming: there wasn't any. Literally the only times I ever ended up on a team were in Alerts/Rampages/whatever those things were called.
3. Gear: the whole damn game was based on what gear you had, and the in-game 'economy' is based around the same money-grubbing tactics used by games with in-app purchases. You could (try to) make the case that CoX's Invention System is the same thing, but you'd fail. In CoX, you can earn whatever IOs you want by just playing the game (Merits), and not worry about needing to spend actual money for THE CHANCE to get whatever it is that you're after.
4. The Community: CO's community pales so badly in comparison the CoX's that it's barely worth mentioning.