If we get to the Plan Z stage (and to be honest, this is much closer to the middle of the alphabet anyway), we're going to have a hundred visions of what City of Heroes "needed" and what the "real spirit" of the game was. And both of the purist approaches -- design by democracy and design by dictator -- will destroy the community.
There's also, and this factors into my thinking on the subject on a creative level, the Champions Online problem. Champions has most of the things you mentioned, fascists, giant monsters, etc... but it doesn't have the feeling of history that City of Heroes got largely by making a bunch of really fortuitous mistakes and trying to make it look like a dozen different stories were really the same story. We can't just replicate that organic feeling whole, and just "making mistakes" isn't going to cut it, either (because CO made plenty of those too). What we'll need, far more than an author (I'm an amateur author and so are a thousand others) or even one story, is a really really good gardener. Somebody who knows the art of cultivated chaos. (And no, I'm not nominating myself for this job.)

It needs a backstory and a hook, and a SOLID universe with storytellers who can run with cultivated chaos, pick it up, and change it on the fly to improve the game. It needs a flexible story that can suit multiple people, with a flexible sandbox that allows people to choose between nothing but outside play, nothing but instanced play, or a combination of the three. It CANNOT have just the "Go, hunt, kill Skuls" type of outside missions, nor can it have just the "I need 10 Skull Masks" types. It needs to have choices of "The city needs you for this, this, this, or that. Please do any combination of them, then call me" outdoor missions and "Go do X in Y location" instanced missions.
I can do cultivated chaos. That's what LARP storytelling IS. I can do stories with 6 possible endings based on player choices plus a "Oh, I didn't think of THAT" response.
So far, my vague idea is "Phoenix City", an area that just suffered some kind of apocalyptic event and is in the middle to late stages of rebuilding, with several groups of contesting bad guys who are trying to take control over various aspects of rebuilding/city life/criminal life. If the world looks like it's suffered a catastrophic event, the art designers and programmers would need to code it for either phasing or easy alterations at various points in the game as the world progresses - keeping it an organic world. I'm not sure how difficult it would be to change contact conversation based on world status from a coding perspective, but that would be something I'd find ideal for creating a more immersive environment. (Trying to avoid the "We redid this zone but we have to redo this zone still" problems that many MMOs have had with later content...and no, I don't know whether that part is even possible.)
I'd defer to the techno folks as to whether an open-server environment like in CO is easier to handle than a closed-server environment in the current COH/WOW/most everything else model. But that would be a major point of how to handle the world-building and on-going storylines.
It needs a starting zone that teaches you about the game unobtrusively, is easily skipped for experienced players, and is fun to play for new players. That's part of the hook. It needs GOOD mid-game content with enough options for players to play through at least 10 times without repeating enough content to bore them. (COH did have a consistent problem with that.) It needs a solid end-game that feels like progression, with goals that make sense for heroes at extremely high levels. It absolutely MUST have a good sidekicking system. It also needs very solid, fleshed out villain groups, and the ability for players to play villains as well as heroes. I think giving players the ability to select a villain or hero group to align with at the start OR be independent would be ideal, and allowing them options to change their alignment, whether it's within villain groups or over to rogue/vigilante/hero.
This is just off the cuff thoughts, mind you. I've only given this a little bit of thought so far.
