1. Allowing LFR to give the maximum reward for casuals/alts. There should be something with similar reward levels that doesn't take up this much time. Most things should have a good effort vs time spent vs reward ratio. LFR scores extremely poorly in my opinion with extreme time requirements (queues up to an hour, followed by up to several hours clear time), no effort required and highly RNG rewards. Getting nothing but gold when coining every boss and ending up with nothing but a few motes of harmony while guild chat is filled with people obtaining LFR items is very discouraging.
2. Stepping away from Cata's JP/VP system and making JP useless and VP for outdated items and item upgrades. I loved being able to buy current tier epics for Valor and previous tier with Justice. You rarely ran out of things to buy with Valor on alts and there was a BoE Valor item you could sell with excess points.
3. Item upgrades and thunderforged/warforged. Both cause unneeded item level inflation. The latter only adds even more RNG to loot. They said they would keep item upgrades in for WoD but at the same time they are removing most gem and enchantment slots and reforging because it was just something you had to do for each item.
4. Giving Challenge modes, and to a lesser extent Proving Grounds, only cosmetical rewards. Both are probably the most unsuccesfull features added in MoP.
5. Timeless Isle. Useless for geared characters (other than farming for RNG pets from RNG rares) and awful "effort vs reward" for characters hovering at the ~500 iLvl.