So far noticed:
Qiraji Guardlings are now in, down by the AQ gates (caught one, no weather effect was running)
Instead of a net you now throw a wooden cage, and the door swings shut when they are caught.
Summoning bug is still there (it auto summons your first battle pet when you try to summon a different pet, or when you zone etc)
When against an enemy pet which is strong or weak to a move of yours you get an arrow (green up or red down) indicating it.
It costs money to get your pets healed at a stable master.
At the end of the battle an effect called Battle Recovery triggers, restoring some of the health your pet lost in that battle.
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Edit: Note - If you did not learn Pet Battling back when it was availble you will stil not be able to learn it yet, they upped the Lv req to Level 91. They have advised they are not ready for testing yet.
June Patch
Re: June Patch
Tricksy, tricksy developsers... I wants to battle with my Precious! 
Also, and this is important (in my opinion), you can no longer attack critters that are marked as battleable... It just gives you the "wrong target" and "you many not attack that target" messages when you try...
Also, and this is important (in my opinion), you can no longer attack critters that are marked as battleable... It just gives you the "wrong target" and "you many not attack that target" messages when you try...
Re: June Patch
It should also be noted that they buffed the health of pets to correspond with their level. Before this patch I was merrily running around and capturing everything in Pandaria. Now they pwn my face. D: Guess I've got to get back to leveling!