Sorry if I'm late to the party but here's my two pence.
After trying out Champions Online for a bit, I can decisively say that I'm much more fond of CoX for several reasons. Firstly, CO's lore was just...well, obscenely generic. I get that they were going for a silver agey feel, but the NPC's are ridiculous cardboard cut outs and I can only remember two of them. Kevin Poe and Doctor Destroyer. Sure there was voice acting, but it was bad, really, really bad.
But with city of heroes, I actually wanted to care and learn about the setting. I actually wanted to delve into the story of things and try to make my characters work in it. I like how, even though superhero settings are often mocked for not really making much sense, City of Heroes, due to being built from the ground up, was in my opinion, a more sensible and well thought out setting than either Marvel or DC.
Also, teaming up in City of Heroes was not a monumental exercise in frustration as is common in many other games. It didn't matter what level you were, everyone could pull their weight and everyone was sidekicked or exemplar'd to an appropriate level. The lack of emphasis on the holy trinity of MMORPGs also made pick up groups far more diverse and entertaining and honestly was more reminiscent of D&D than the standard MMORPG formula.
That is, D&D without the ridiculous imbalance of the classes (I'm looking at you Clericzillas and Batman Wizards). Which made every team up, every get together unique and exciting. It was far more fun to be kicking ass with a kinetic controller while explosions were detonating everywhere or a force fieldy defender than it was to just have some big brick soak up hits, a wizard flinging a fireball while a priest just heals people up.
I especially love how colourful the battlefields in CoX get at high levels as everyone lets loose with some of the most fascinating to watch SFX combinations in a game, nevermind a MMORPG. The entire world just seemed to *work* and I was glad to play in it and study it in depth. And I was tremendously saddened when it all went away.
Also, the Character Creator was amazing and always seemed to let you make just what you wanted, while things like DCUO and CO tended to have a certain "aesthetic" that you had to keep to even if they technically had more options like in CO's case, or in DCUO's case they actually had *less* options. Try as I might, in CO I could never quite make a character who didn't look too...cartoonish for what I had in mind.
Nothing else just...clicked so well.