Hunters get some love in the upcoming patch 1.7—as revealed by Caydiem, Wow Community Manager:
All right, folks, here’s something that should lift your spirits. The following are the pet customization changes in the 1.7 patch.
You can now train your pet in passive abilities such as increased Armor, Stamina, Fire Resistance, Nature Resistance, Shadow Resistance, Frost Resistance, and Arcane Resistance using their training points.
In addition, there are specialized abilities for certain types of pets:
Bats, Owls, and Carrion Birds can now learn the Screech ability, a fast, single-target attack that also lowers the attack power of all enemies within melee range of the pet.
Cats can now learn the Stealth ability. In addition to being unseen, they receive a damage bonus for their first attack coming out of Stealth.
Scorpids can now learn Scorpid Poison. This poison deals Nature damage over time and stacks up to five times on a single enemy.
Wolves can now learn Furious Howl. The howl adds a flat amount of damage to all nearby party members’ next attack (within 15 yards).
The training point costs for all pet abilities have been rebalanced, and Growl is now free for all pets. You can untrain your pet’s training points from any Pet Trainer in the major cities for a fee. Similar to talent respecs, untraining a specific pet scales up as you do it more times: 10s, 50s, 1g, 2g, 3g, etc… capping at 10g.
Hunter pets will now gain experience based on the level difference between them and their target, rather than the difference between the Hunters and their target. This will make it much easier to level up a low level pet. You will still need to kill creatures from which the Hunter can gain experience, however.
And lastly—as a comment to an annoying issue for many—you can adjust the autocast status of skills with that option in the spellbook.
The designers are looking into further customization, but this is what is coming for 1.7.