IMHO the best PvE gear should come from both, PvE and PvP, and the best PvP gear should come from PvP and PvE. That way only the best players get a true BiS. Gear aquisition will be balanced that way, too.
Edit: just to clarify, I meant that a true BiS would be a combination of PvE and PvP pieces, not that you could pick either and it wouldn’t matter.