1. LFR. It is just horrible. Brain dead simplicity that still causes failure and utterly unpleasant behaviour. These people who rage quit and spew nasty shit in chat obviously do not want to work with people so either cut the mode completely or cave into their behaviour and make it completely impossible to fail. Either way, do not make it any kind of requirement to gear up for organized raiding. Nothing is more frustrating than having to run throne of thunder LFR over and over to be able to go into the normal mode due to gear requirements.
Things are better with flex being your option, but a lot of teams still demand ilevels better than the catch up gear available. LFR is the biggest thing for ruining MoP for me. I sprinted out the gates but life happened and I fell behind. Having to do LFR made me sick of the game before I got to do the content as it is intended. I much preferred the model of having 5 mans drop equivalent of the last raid tier than running the current raid in brain dead mode to get the gear to run it at a fun level.
2. Letting arena balance affect pve. They already shut down some abilities in BG's and arena, just separate everything already. Neither game type benefits from the other. Just balance them separately and remove abilities that are problematic in one game type only.
3. Making dungeons retarded. This is not just an issue with end game heroic dungeons, it is systemic throughout the levelling process. Dungeons are utterly face roll. Some classes can solo them at level which breeds lazy players who just /follow the prot paladin through the instance. I'm completely fed up of afk dps and healers in full heirlooms dpsing and not healing because they assume all tanks are immortal when monks in particular are susceptible to damage spikes and have poor self healing at lower levels.
4. The story. It died with the Lich King. Too much self and pop culture parody and not enough drama, conflict or new and interesting characters. The parody stuff has got out of hand with Uldum and a lot of Jade Forest and Valley of the Four Winds is just irritating. There's some good stuff there too, but it is ruined by blizzard quest designers trying to be funny. Uldum just makes me so angry.
I think using time travel to bring back old characters is both lazy and stupid. Warlords has a truly cretinous premise. They seem to just be dismissing everything too. The fact is the idea is so full of holes, paradoxes and other such problems but they are choosing to ignore them. When events don't work in terms of believability within that world (fantasy has to be as real to its rules as possible because of it's subject matter and thus good fantasy is dripping with realism because it cannot break from what is believable without losing the audience to doubt) the world breaks down and becomes ununified, uncohesive and people no longer believe in events that take place within it.
Warlords is an exciting concept, but one that just doesn't work. From all the sound bites from blizzard employees, it appears they are just ignoring the integrity of their work for "cools" and this is utterly and indefensibly wrong.
5. Nerfing current and previous tiers. GEAR DOES THIS FOR YOU. Of all the dumb things, this is one of the dumbest. I am in a reroll guild at present and nerfs along with relative player power increases at the old level caps make old raids comparable to MoP 5 mans in difficulty. It's great when a boss has mechanics that don't scale with player power and remain dangerous and needing coordination, but those are not many.
When I restart MoP content with this guild in a couple of months, I am going to find the content much easier than I would have if I was playing it when it first released even with gear restrictions for each tier. It's okay to nerf something if they have clearly overturned it, it's not okay to nerf so that players can complete a difficulty mode they don't deserve to finish. It completely ruins the raids for latecomers.