This has been discussed ad nauseam. There are threads for it, and there are discussions of it buried in other threads.
Some of the problems I've noticed:
Any centralized system means someone is at the center. That person can potentially ban at will from all servers(depending), or quietly remove bans, or finagle accounts, change accounts, disable accounts, etc. How about a server operator pisses off the master server operator and then has their account vanish? Is there any recourse? Now you need a whole jury type structure to handle such disputes. Wait, I'll run it. Crown me the king of tremulous!
Different master servers for different versions? Buh Bye tremulous.
All servers are donations, essentially. If I run a server, why should I relinquish control of it to others from other servers (who will also be banning people)? Why should you trust me to not ban your friends from my server? (and ultimately from your server) Why should I trust that some centralized system is fairly handing out accounts and cannot be abused?
You can't stop me from setting up new accounts. Its open source software, you cannot run anything on my machine that I can't manipulate, much less manipulate the source code of, so thats out.
You cannot set up a system with enough integrity that doesn't also abuse my right to privacy. Want to see a bill to verify my address? Noone would do that, suggesting it is silly

.
Restrict email addresses to something? Think of any combination of letters you can imagine and multiply it by the number of root domains. Now, make a list of which ones are allowed/disallowed. Make an exception for gmail or yahoo mail? Now its even more worthless but it still takes 47.8 hours to parse your domain list.
Ultimately, you can't make a system that doesn't centralize power away from the server operators in a way that is acceptable to the
server operators. The closest thing I've seen is a web of trust idea, where servers can choose to share a system (or not). But telling all server operators that someone else will be deciding who can/cannot play on their server is just silly and would never work. A web of trust at lease allows friendly server operators to share bans/admins/whatever, but wouldn't require it.
What it really comes down to is: If banning me from one server doesn't ban me from all servers, and I can make a new account, what is all this work for?
My last question, who's paying for all of this? You'd need strong keys so admins/master server operator couldn't take over accounts, centralized authentication, etc. How fucking big of a server/pipe do you expect someone else to donate so that you don't have to admin your own server? Sure, looking at keys is easy. How about looking at 1000 of them? Strong keys would be larger, more bandwidth. This game isn't exactly kept alive with donations to the site you know.
Alright, so this is pretty disjointed and not very eloquent. I jump around varying concepts of what such a master server would be without actually pointing out that every argument may be the result of a different concept of such a server. I may search for more later, when I'm awake and have more time.

Just think of some of these as questions to ask yourself no matter what kind of master server you envision.