So here's the deal, you're asking on a CoX message board why CoX is better than CO, so of course you're going to get a lot of biased feedback about certain features CoX fans prefer over CO's implementation. I'll freely admit I'm biased too, after having had extensive experience with both games. However, there's a simple, unbiased fact that I think gets to much of the heart of the issue.
During CoX's "live" period, the game developers (Cryptic, then Paragon) *never* stopped adding to the game. They were constantly adding new power sets, zones, story arcs, features, costume parts... Even right up until NCSoft pulled the plug, Paragon still had huge new content in development (some of which the SCORE/Homecoming team has been able to implement into the current issue of the game). Heck, CoX had TWO full expansions released during its run, which dramatically increased the size of the game and amount of content it offered.
Contrast that with Champions Online. Over its entire lifetime, very little new content was added. Almost all of the development in that game was focused on the cash shop and the loot boxes. I don't know if it was a matter of financial constraints or simply biting off more than they could chew, but Cryptic added very little real content to the game for players to enjoy, and what WAS added was primarily microtransaction-based. Champions Online had a lot of wasted potential, and part of the issue was that Star Trek Online stole much of its thunder (and developer attention).
Which game had better writing is a matter of opinion. Which graphical style looks better is a matter of opinion. Which game's "tone" is better or more engaging is a matter of opinion. Which game had more content is a case of fact, not opinion. The dearth of new content for Champions Online had a demoralizing effect on its early community. Promises made were slow to deliver, and many were never delivered upon at all. People lost interest in the game as they completed most of the content on repeated characters, and little was done to stem the tide of players leaving the game. The free-to-play button was pressed to try to bring in new blood, but that brought other deep problems to the game as much of it was locked behind paywalls. Champions Online has been on life support ever since.
It's really a shame. Cryptic was unable to capture lightning in a bottle twice, and once the game began spiraling down there was little that could be done to save it, especially with their main resources dedicated to Star Trek Online. It's literally A Tale of Two Superhero Games; City of Heroes/Villains was beloved by players and by its studio, but the publisher pulled the plug unnecessarily and killed it before its time. Champions Online was neglected by its developer and abandoned by the larger MMO community, but its corpse is still shuffling around waiting for its mercy killing.