No matter what game your playing their are always going to be favored classes/specs. Just because there would be a lack of balance doesn't mean that bioware shouldn't incorporate a new fun pvp aspect of the game.
Arenas are the epitome of skill based PvP. There is nothing that would require more skill, thought, and communication in this game other than ranked warzones. Ranked warzones even would have the same balance issues themselves, have you played wow's ranked bgs? All the best teams generally use the same setup of classes to be able to reach the highest rankings, and in a game like this there's absolutely no way around it.
So say what you want, but having experience in high-level pvp in wow, I know that even though there might be some teams that are favored more than others, I would still like to see the arena system implemented simply because it is probably the best competitive pvp for an MMO you can get. (No competition = no fun)