What in the world is causing such a huge discrepancy between hunters and other classes when it comes to high-rating arena representation? When I play in Arenas and Battlegrounds, I don't feel like my class is somehow deficient or underpowered. My team's Arena rating is average -- we're not the best, but not the worst either. When I get beaten, I usually feel like the other team actually played better (or outgeared us, at least), so it's rather hard to see what's so messed up about hunters.
The most obvious issue I can think might be the issue is that of Line of Sight. Hunters obviously have a rough time shooting at things behind sort of obstacle. In battlegrounds there are more wide open spaces, so it seems less of an issue there, but in Arenas it can get fairly annoying. Classes like warlocks and shadowpriests can just put a damage-over-time spell on you, and then hide behind a pillar, while druids can move freely around obstacles to give them plenty of time to heal themselves between your attacks. Warriors and other melee classes can hide for a bit, then get in so close that you can't use your best ranged abilities on them for a few seconds until you can somehow get away.