I hate RNG on misses. A miss of 90% hit spell with 5 sec CD like Nether Gate used against pet that is strong against you to swap it out means more often than not that you lost, unless enemy have similar fumble and you don't.
Even worse are RNG cc's. 25% to stun your pet? Of course it will happen, here have 2 turns disadvantage.
I dislike how only Rare pets matter and everything below is just fodder. I'd prefer if all pets have same power in stats (still with different breeds) and rarity/colour was something gained by amount of kills done by said pet, sort of rank system.
I dislike how people can forfeit once they see your team without penalty. You should get at least 5min deserter debuff if you chicken out, and even early escapes should give other team win.
I hate how much Sandstorm hard-counters dots and multi-attacks. I understand that Aquatic Crab with Shell will not feel dots, but I don't see why a weather effect should have such strong effect over 9 turns through pet swaps. And next patch, Elementals get to use the effect too, guess what group of pets have most Sandstorm in their arsenal? I don't mind weather designed to help against such things, but it should be at best a 50% version of shell, otherwise running dot team is insta-loose against Anub Idol or Sandling, similarly Swarm like skills are complete waste.
I dislike how anti-dragonkin is current meta. They get slaughtered by humans. To counter humans, undeads are used, which dragon attacks are weak against. They don't take much damage from flyers, but there is very few of them that are good, and most run with Crow/Raven with Darkness, a move that is nuke good against dragons. Magic pets are quite rare (oozes due to anti-dot sandstorm), and if they happen, it's usually a broom that can swap your dragon out. And even further, magic pets racial works against big hits, something dragons are build for (+50% against magic, +50% racial active) which kinda negates its main strength.
I dislike how Blizz still haven't fixed AH UI. Previously, ticking 'can use' box would filter out pets I already collected. Now I have to sit through all of them, 2 lists even for some reason.
I dislike how pet biscuits aren't account bound, if my alt needs coins I have to clear dailies on it, then log main to collect bags.
I dislike how on pvp realms, gankers have upper hand over you. If one attacks you, you are forced to close battle to have even chance to not die. No matter what you do, they always can make you loose the pet you are trying to capture, and there is no way short of having 1-2 people guarding your back to not get griefed. At least make pause option so once I kill him, I can go back and finish battle.
...so yeah, lots of things I would like to see improved on. I still love pet battles anyway, and hope they will fix those things in future.