You're right, I enjoy my full PvE BiS hunter in Alterac valley the most, if you play carefully and don't expose you, you will kill the guy you focus in less then 6 secs with a Serp sting- chimera shot - aimed shot - arcane shot - Kill shot. I know some of the alliance players and I focus them sometimes, I know they are BiS geared and I still do 10k crits with chimera shot when the trinks / cooldowns procc, I haven't noticed any change on my damage as "Hunter" but I guess people realised that BG battles end so fast it's nothing like a 1v1 when your both prepared, so a lot of people go with a lot of PvE pieces to boost their damage, and if you get into a 5v5 in Arathi basin you pop your offensive / defencive spells and try to nuke them quick, it rarely last longer then 20 seconds until the last guy goes running.
Some BG's i se more glass cannons then anything else.
On my Unholy DK I tried to go full PvP (2 piece from bis) every single piece, and I started having a really hard time killing people due to the low damage output you get with only pvp gear on. I swapped more then half of it for BiS PvE pieces and I suddenly I took down several wrathfull Holy Paladins in 1 burst.
PVE gear is superior even in PVP. AS LONG AS YOU CAN SURVIVE IT, thats the thing, you have to be able to survive too.
The biggest secret to pvp is practise, know your class inside out against every other class ability, if you can counter the things your enemy is going to throw as you, then you don't need the extra surviveability all that PvP gear gives. It takes a really long time to become truly good at pvp on WoW.