Play with your friends. If you are playing on a pve server, you're more likely to be interested in pve endgame than pvp, so the server being overpopulated on your side isn't going to be a bad thing. I don't really think it's ever a bad thing to be on the more popular side, it's not as if battlegrounds are only for one server any more.
I play with friends from uni, and I have more fun with them than I ever had raiding (up to MH and BT).