The point to shared servers would be: that's what MMOs are. I wish it was more interesting of an answer, but that's all.
That makes sense (as does the other stuff you posted, but I don't want to address it). I hadn't really thought about the nature of the "massively" part of MMOs as intrinsically tied to a shared server. There's no incentive for an MMO developer to make the game available to players who want to run private servers, because then there would be no incentive for said players to log in to the shared servers, and there goes your MMO. But I think that if you're a developer and all you want is a robust community - whether they play together or not - shared servers don't matter.
I think a cool thing to do would be to make a single player game, with a few characters to play through some select storylines that tie in to the MMO. Then the MMO allows any character, any mission to be played. So in CoH, I guess it would be more like a longer personal story you could play on CoH - for example, as a single player you could select Apex, Horus, or War Witch and play through the storylines from their comics. Then you go to the MMO, and you continue the story of your own character within Paragon City (most of the comic storylines take place as introductions to villain groups, so it would be cool to see how they re-emerged in Paragon City before you start the MMO's story). Gameplay, graphics, everything would be the same, but in single player you can only be one of the three characters and you only get whatever contacts / missions that would be made for the game.
Although more practically, with the current situation of a CoH MMO not existing anyways, private servers are the only way to go now, and there's no developers to incentivize playing on a shared server. I imagine that if something gets off the ground, there will be multiple private servers, and a few will rise to the top: a "standard" CoH, running the game as it was; and a few "modded" CoH versions, with particular players making the changes they want, and the most popular changes get played the most. Regardless, the community (such as is left) will still be robust.
Edit: A kind of cheap way to "incentivize" playing on a shared server is making the game have lots of group activities, that require other characters to complete. So on a private server, if someone doesn't have enough other players, they get NPCs to help out. The devs then make the AI really dumb, so it's all but impossible to complete these group tasks without other players.