Trying to balance a game for PvP and PvE is nearly impossible to do. I totally agree with you.
Arenas and PvP in World if Warcraft destroyed the game and lead to the homogenization of the classes.
Borderlands doesn't really have PvP and so the PvE design is free to focus in fun even if things end up overpowered. Their design mantra was, "is it fun? Yes? Then -BLAM- it! Just make it fun!"
For PvP to work things have to be balanced. Otherwise it's not fun. The outcome is most certainly the over tuning and sacrificing of fun for game mechanics that could easily be left alone in PvE.
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