The trouble with PvP is... well, there are several problems with PvP. The problems of balance are always there, of course, as they are in every aspect of the game. There are the problems of making PvP both accessible to new players and rewarding for veterans, their are issues with keeping people engaged in the game without being gimmicky, there are issues with even such little things as how players get equipment. But as Scott Jennings notes in his most recent column, a lot of the problems with PvP-centric games center around perceptions -- both those of the players, and those of the developers.
Developers who make PvP-centric games frequently are players of games themselves, of course, and so when they strike off to make a game with "PvP done right" they can sometimes fall victim to tunnel vision regarding their game. (Jennings cites Shadowbane, Darkfall, and Fury as examples here.) But there's also a problem of perception from the player end, as whether or not a class is overpowered often pales in comparison to whether or not the players believe it's overpowered. From Guild Wars to EVE Online, every PvP game has had to contend with these issues, so it would be well-advised to take a look at the full column if you're at all interested in the design of games.