Why don't they just setup 2 different skill trees, containing the same abilities but one is balanced for PvE and one for PvP? Seems like it could work to me. Just implement a system when you can't PvE while in PvP spec and vice versa. That way nothing in PvP has to be op because they won't nerf it because of PvE. And you will of course be able to set both at the same time. When you enter Arena it switches to PvP spec or whatever. All the other time (unless they allow non-arena private duelling) you run around in PvE spec.
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