I honestly think both games had/have their Pros and Cons. And both are 'good' in their own way. The do vary in some key areas, but without that variation, you would have nothing but a cloned game, maybe with some updated graphics.
CoH/CoV had:
Better and more rewarding team play
Better overall map design
Better character choice (Choose Hero or Choose Villain)
And the moral compass in me can't forget the lack of MTX
CO had:
Better selection of costume parts(Most locked behind expensive MTX)
More definitive 'gear' over the 'Enhancements' that CoH/CoV has
Vehicles and Vehicle 'End game' raids (Also accompanied by MTX) (Though why some 'Super Heroes' need a vehicle is beyond me. You never saw Superman driving in a car normally)
Teaming up was usually reserved for 'end game' raids, and near the end of the game it was more; 'Hop in an alert queue over and over to level as fast as possible then wait in more and longer queues to try and get the raid you wanted/needed'
Oh and the voice overs, please for the love of everything unholy, I wish I could forget those horrible cheesy voice overs
Personally I think CO was more 'geared' to attract the 'WoW Population' and CoH/CoV was more tailored to the gamer/hero/MMO audience. It was all a shift in 'gaming culture' that made the 2 different.
On a side note; 'MTX' means 'Micro-Transactions'. Just for those that don't know what that term is.