Though I understand your thought Phantom Mouse, Multiple Man character could also consists of Multiple Man 1 to 100 so that won´t be a problem
And if you are Electro (just using a existing name for the example, I know

) why not being Electro2000 or Electro-Omega?
Whatever, I understand, that some people here do have the fear, that they will be restricted in their freedom of creating their character with the name they have in their minds.
Others fear, that the promised Indivdiualsm of their characters will go to hell! I will not say, that any side is wrong, because they are not!
When I stumpled over CoH the first time the game was around for a few years already, so I had to live with the fact, that some typical Names where not available anymore. That kind of frustrated me, because I wanted to play the characters I created in my own universe in that game. For example my comic universe got an Angel - for CoH I renamed her Ayara because Angel was taken already (what a surprise). A short moment I was kind of annoyed but I got over it very fast. And in looking back I have to say, I would not have wanted the Angel name if that would have meant, that I am one of numerous Angels, because that wouldn´t have given me the feeling neither
Now I don´t want to be the pessimistic guy here, but I believe it will be a while before we even have to really think about getting out of names, to tell the truth I think it will take a while until we have to be creative at all. And creativity should be a basic tool for people who live in a superheroic backround anyway.
And though I understand, that there is only supposed to be one server I think it should be considered if more servers could make sense eventually in reasons of gameplay. I mean, I am not the greatest Villain Player anyway, but if I think about the approach of CoH I think they did it wrong! Of course it can be fun being in a City of Heroes and trying to do your stuff underneath their eyes (which never happened anyway - I mean otherwise Villains would have had to walk the same areas and would had to be free for attack) - and having a part of a City or Ship of Heroes which was taken out of control of the Heroes and is a law free area can work a bit.
But haven´t we talked about an extra ship of villains a while ago? It would make sense, as I see it, if they have their own server since they got their own ship too. And therefore, there should propably be a third PvP Server where Heroes and Villains (and those in between) can kick each other into oblivion as much as they want. All of that of course goes a long way down the road (as Ship of Villains too) and until then the community will hopefully be big enough to make us think about it).
That will as I see it also not lead to Server Rivalries because the Servers serve different purposes anyway.
Back to the topic - of course you could have a plattform, where you have several people using one name and if you klick on them for contact or whatever you see who is behind it
But I believe that will kill the feeling of that "Universe".
I mean, all of you have talked about having individual names or having the name of your choosing, but have you considered, what makes kind of the feeling at DC or Marvel for example? You see a costume and you know that is Spider Man or Superman and you know - or think you know everything about it - that created their legend and legacy. And I don´t know if there are exception but believe me I know nobody who wasnt in given time pissed about those confusion storylines where people wouldn´t know who is the real deal in the story. Anyway, my point is part of the feeling being a Super Hero (and what didn´t work at DCUO) was, creating your legend, your legacy! And how should you do that, if your name is not one of a kind?
Yes, I know people could notice who are around because of the costume - what if I change the look? One could klick on the caracter and see the number - who likes to do that all the time (not me, not for that reason)
It could be visible all the time - well then I could name him Elektro 2394 from the beginning where is the difference?
I think the question is what is more important - the individualism, which creates legacy (and creativity)
or the freedom which creates - well freedom to name it
And as many might have guessed already - for those who don´t I make it clear here

- I vote for the individualism and accept, that if somebody else takes my whish name I have to do what any comic company has to do too - think about another name.
Because I don´t believe your character would feel unique, would feel the same if you know there are others around who could be mistaken for you even if they might not be online at the moment.
(though it might be an idea to have a time limit included - so if somebody won´t go online for a certain time which has to be thought through of course, which hints that the player might not play anymore - the name will be available again)
What is Reality, what a Dream? Is the dream changing your reality or is the reality defining your dreams? Only one being aware, that awareness can never be complete can use both to become the best possible and combine both to form the future! PDM