Personally, it wasn't really a question of which was better, so much as the fact that CO, despite it's namesake, had little if any resemblance to the pen & paper game I enjoyed so much.
On top of that, the gameplay experience in CO felt woefully un-superheroic. I never felt like a hero in CO at any level even approaching the heroic feeling engendered by CoH.
There were some things that I liked about CO, but the UI wasn't one of them -- it was very plastic and unappealing. The stylized look did not endear it to me.
Anyway, it was for those reasons that I failed to stick with CO, whereas at least some of the reasons that I would continue to return to CoH are probably inexplicable.