Hi fellow Hunters.
I am a reasonably new Hunter and I have some questions.
I am a B/M Hunter currently using a Spirit (Gon) pet and the Sewer beast.
For Mythic/Raiding what 2 pets should I use, and can you use 2 different pets, like one spirit pet and one tenacity pet?
Does the second pet get it’s own separate abilities or is it only the primary pet?
What is the best combo for highest DPS and does it change for AOE vs Single target?
Thanks in advance for help 
Second pet doesn’t get special abilities. You just get one pet family.
Best overall pet for dungeons and raids is a spirit beast, unless you need to bring heroism in which case a ferocity pet will be what you use. A clefthoof is good to have for solo content as it has great survivability.
It’s always a good idea to keep one of each pet type in your Call Pet rotation. Here is what I use:
- Tenacity pet - Spirit Beast: Gives extra health, and an extra heal/defensive. I macro Spirit Mend to cast on me on cooldown. It’s not much of a heal, but every little bit helps.
- Ferocity pet - Clefthoof: Mostly used when you are responsible for Heroism/Bloodlust. Clefthoof helps if your pet tends to pull agro on packs of mobs. They are less likely to get insta-gibbed than other pets.
- Cunning Pet - Any: Situationally used when you have need of extra movement speed and/or more ways to remove movement impairments. Proper use of Disengage makes Cunning pets mostly useless in PvE though.
Your second pet doesn’t get any additional abilities, so it’s really just a visual thing. Use whatever second pet you think looks good.
In modern WoW individual species no longer matter nearly as much as they used to. The only thing you really need is 1 pet of each “family” (Cunning, Tenacity, Ferocity)
As others have said, Clefthoofs are “technically” the best species overall for most content due to the specific combo of pet family and their species specific abilities but the difference really is super small.
You’re mostly correct, but the difference between Clefthoof and other pets is staggering. The defensive and self-healing capability of the Clefthoof just makes it superior.
When I’m soloing Zaralek Cavern rares, I don’t even need to heal my Clefthoof, yet I have to rez every other pet multiple times in a single fight.
In M+ dungeons, if the tank is bad at AoE agro, my Tenacity Spirit Beast will pull agro and fall over dead at the beginning of the pull. My Clefthoof takes it like a champ.
Of course, you probably already know this and just downplaying the difference in hopes of avoiding the pet getting nerfed. Well, no worries. Blizzard doesn’t read these forums. 
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No I actually didn’t know the difference was really that massive, my main pet is my beloved Loque’Nahak Spirit Beast and I keep a “The Kurken” Core Hound if I’m somehow the only one who can lust in a raid or dungeon group
Why does Blizz not nerf them or buff other pets to make the choice less 1 sided. From what I’ve read Clefthoof has been the default best pet literally since they became tameable. I get Blizz hates hunters, but that just seems a little goofy
Probably because all Tenacity pets should be as good as the Clefthoof, but they don’t want to do the work to make that happen. It doesn’t do more damage than other pets, so survivability isn’t really an issue that needs to be addressed.
Also, Clefthoof models are large and annoying to many Hunters, so not many Hunters actually use them in most content.
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Because the difference is largely meaningless in anything other than solo content. And even there a clefthoof is not needed the vast majority of the time - any ferocity pet will serve just fine in most places.
Pet damage is standardized and the pet does not matter. As for raiding and mythic plus I actually don’t use a spirit beast. Their healing ability is really too low to even care. I like to use a bear as they are tenacity, which will give you the fortitude of the bear ability, also they have a passive defensive ability that reduces their damage taken when they reach 40% hp. This has actually saved my mythic plus groups multiple times when our tank dies and prevented wipes, As my pet can take aggro and give us enough time to brez the tank. Petopia is a great website to go to as well if you’d like to learn more about pets and where to find them.