My suggestion is quite simple.
CoH felt good, we liked it, and miss it. Replicate the design as much as time, finances, legal concerns, and tech permit. Redesign only the smallest portions of the wheel that are strictly necessary. See what kind of game you have and gradually fill in the blanks.
With all due respect to those theory crafting, I don't want to play a superhero MMO as they would have done it. I want to play the one we had. The other heroic MMOs that have popped up on paper look very similar to CoH. The differences are smaller than many of those suggested in this forum. But those games have not by and large filled the gaming needs of the former CoH crowd.
Obviously we cannot have the exact game we lost, but let's not make it any more different than necessary.
To put it another way. Give us a clone with facsimile errors, not a bizarro world twin.