http://www.wowarmory.com/character-sheet.xml?r=Shu%27halo&n=Nathaniel Improved Hunter's Mark adds to your pet's DPS. I do miss Efficiency though, but you'll compensate on certain fights by switching to Aspect of the Viper and timing your Mana Potions right. I picked Animal Handler instead of Frenzy because of the +4 chance to hit with my pet. I actually found it a toss up between Improved Mend Pet and Improved Revive Pet, this one might come down to preference and/or area of play. I am on Steady Shot/Auto rotation.
Indeed it's true that BM Hunters rely more on our pets than other builds in terms of providing added DPS, and that in some fights, pets will die from AoE damage. This is alleviated by knowing when and how to properly pull your pet prior to the AoE damage killing it. Usually, if you see your Melee classes pulling away, you should pull your pet out from the fight too. If you know the fight, or if someone in your guild can kindly tell you when to pull, you will be able to save your pet. Most times, you are only going to sit your pet for a bit, and you will be able to send it again. If you keep your pet alive beside you on AoE pulls, remember that you can still use Bestial Wrath.
I am missing a lot of PvE gear due to being new to raiding, and I need a lot of improvement in terms of gear. I've only cleared Karazhan 4 times, 2 of them in the span of 3 nights, and the other half in 2 nights. I have yet to see Legacy drop, and Attumen has not dropped any Hunter gear on my runs so far. I am trying to compensate with adding +hit and Agility gems on my slot, if I can. I am trying to collect the mats for the +28 crit right now.
Good luck to all raiders/PvP players out there, and thank you for the posters who provide accurate and proven information on this site.