I agree with this a lot. Though I know there's a fear of splitting the community too much I'd personally like to have total control over my own server than play on a hugely populated one. Plus, the fact is that some of the CoH community didn't really blend. RPers and Non-RPers constantly fought even on Virtue. Imagine if every server was merged into one, mixing every kind of player? That'd be pure chaos to mix all the different kinds of cliques. Speaking of, everyone would pretty much just be hanging out with their SG mates and all anyway. Most social interaction would probably be scarce. Not saying that there can't BE a 'main server'. If someone were to host one for those who can't/don't want to host a server themselves, that'd be great! But I'd strongly advise against making that the only server.
There's a lot to be said for both wide-open public servers and invite-only private ones. When any player at all is allowed to join a server, you end up meeting people you never knew you wanted to play with. I've met some great friends in City that I don't really have much in common with outside of the game. If I had only ever spoken with them through a forum first, I'd probably not have hung out with them at all, and that would be a shame since I'd be missing out on some really cool friends that way.
On the other hand, I pretty much agree with everything you're saying about why private servers would work well. Each and every server could tailor the game perfectly to that group of players, so that they get to play their perfect game without having to be interrupted by events and players they don't enjoy. The one and only hitch with that is, you only ever get to play with people you already know from somewhere else. You're protecting yourself from the things you don't like, sure, and that's great. But you're also preventing yourself from finding new things that you didn't know you'd like until someone else asked you to try it.
For my money, I think the ideal solution would be to allow both. Set up one public server with "vanilla" rules that anyone can log into, where players can mingle and find new people to play alongside. Also let folks set up their own private servers with their own adjustments to the rules and the environment so they can enjoy the game their way with their group of friends. (Although to prevent cheating, don't let them transfer those characters to the vanilla server.)
But one thing I definitely think should be enabled is for ALL the servers, public and private alike, to be able to hook up to one central set of global chat channels. Anyone on any server could talk to anyone on any other server, as long as you're in the same chat channel. Stuff like Help and LFG and etc would be local to that server of course, but the global channels would be exactly that: world-wide. Just like how someone on Freedom could talk to someone on Liberty if they were in the same global channel. But this way
any server, public or private, could talk to any other if they wanted to (as long as it was online of course). I think that would help people get the exact play experience they want, while also still allowing the communication that would keep the playerbase at large interacting with one another.