I advise against Crystal Desert. In fact, I'm moving my guild off of there for BWE3. CD was so crowded that it kept locking out new character creation and some people in my guild couldn't get on there for BWE2.
Of course, could be that enough other people will be thinking the same thing and moving away that it will actually be fine...but I'm not betting on it.
One thing with GW2 that's a pain in the ass is that once you make a character, you're locked into that server as your "home world". You can do PvE on any server but you can only WvW on your home world. If your home world ends up sucking for some reason, well, tough shit. Cough up $10 or whatever to buy the server transfer to move your home world. So there's a lot of pressure to choose wisely. (It would be sensible for them to set like a 36-hour free-transfer windows so people can get settled and move if needed but I've heard no word of that.)
My personal suggestion would be to pick one of the servers that opened in BWE2. They were underpopulated for BWE2 but I think they'll fill out as people from overcrowded BWE1 servers make the switch.