Isle of Conquest and Alterac Valley are usually more like PvE than PvP. Most of the time, you are fighting NPC's and not other players, especially bosses. For these NPC's, is resilience useful at all? Or are they just like dungeon bosses? As a warrior, should I put on my PvE tank gear in IoC and AV? In sum, does resilience affect damage from battleground NPC's?
It might be a good idea to have a mixture of the two, especially if you plan on main tanking the end bosses in AV or IoC.
Tbh, on my warrior, if I fancied playing BG's in prot, I always went in my PvE gear, just so I had that extra bit of damage, plus I tanked the end bosses most of the time without too much trouble.
In conclusion I would have to say this:
1) When you're in the actual BG fighting players, wear whatever you feel comfortable with; either PvP or Pv