I played CoH at launch but have since stopped and I recently started playing Champions Online with a free-to-play account. Both games are made by largely the same company and share many common similarities. However, there are slight differences that make each game better in different areas.
City of Heroes tend to be more polished in terms of ease-of-play, graphics and freedom of choice (powersets, costumes and auras, hero/villain, mission types).
Champions Online on the other hand has more cohesive and interesting storylines as well as missions where you do interesting stuff. There is nothing in CoH that comes close to rivaling the stuff I've done in Champion Online's Adventure Packs and Comic Series missions. Another example is in CoH, you never get to play alongside their signature heroes like Statesman, Positron, etc.. whereas in Champions Online, I have both fought with AND fought against Defender, Witchcraft, Kinetik, etc..