Biggest problem with hunters is imo the blatent lack of ulility, especially in 10 mans.
Hybrids are far superior to hunters or rogues or even mages, in MOST encounters. Their flexibly is just far too strong. It helps a ton if you know that you have another raid cooldown ready, if you need it. It helps a ton if you know that you have lineup which can adapt fairly easy by just letting the hybrids respec.
Pure DPS just falls behind in that, as we dont deal more damage than hybrids anymore but offer less raid utility. This is a blatant oversight by blizzard, atleast in my book.
Ele shamans MIGHT not deal the best damage, but they offer tons of utility and if you add the damage from stormleash totem to them, they basically deal more damage than a hunter...