Too many abilities
Back to back Death Grip, two sets of hand spells, Charge > Charge > 30 sec CD Heroic Leap, druid with Blink and Ice Block, monk with baseline Nitro Boosts, etc. PvP was more fun and arguably more skillful when there were half the abilities.
Another problem is abilities just don't feel special anymore. What happened to concentrated coolness? Take Hand of Freedom -- nowadays there's Death's Advance, Phantasm, Burst of Speed, Blazing Speed, and Tiger's Lust.
Too many fuc*ing pets
More often than not there's a zoo on me or in the general area, obscuring my vision. Stampede is the worst offender, but recently the following were added: Guardian of Ancient Kings, Murder of Crows, Demo summons a bunch of imps, hunter and warlock can both summon secondary pets, shaman elementals can be permanent and used in arena, etc.
I've always enjoyed making WoW PvP clips and movies, but whenever I record something in MoP, the game just looks dumb. I don't know how this plays out in PvE, but in PvP it's beyond obnoxious.
Too much stealth
Druid, hunter, mage, priest (Spectral Guise), and a rogue's entire team -- it's just too much. Nerf Subterfuge to only protect from hostile actions because as soon as a rogue opens, he should be visible.
In MoP, just about every class has a burst CD, and the classes that already had one now have two or three. Put these on a shared 10 sec CD or something. Swifty macros detract from the game.
This isn't quite CD stacking, but Bestial Wrath is poorly designed, an offensive CD and defensive CD rolled into one. How is it still around after all these years -- do the devs not remember the effect Beast Cleave had on the WoW tournament scene? Granted, watching spell cleave tournaments towards the end of WotLK was equally boring...
The melee vs. caster arms race is over. We've nuked each other and ruined the game
Mage casts Frozen Orb, Deep Freeze, spams Ice Lance: nice casting, bro. Kil'Jaeden's Cunning. Casters probably need this stuff with how the game has evolved, but nerf it. Nerf gap-closers and gap-openers too. Take away my double Freedom and put Emancipate on a short cooldown, I don't give a sh!t, nerfs all around instead of everyone always getting new toys to keep up with each other.
Nerf blanket silences and then nerf silence immunities. Remember when there was only Aura Mastery? Now other healers have one and so does warlock. Nerf all of this crap. Hunter felt better designed as a caster than a melee.
Some spells are balanced too much around counters
Counter-play is interesting, but do we really need Berserker Rage, Lichborne, Desecrated Ground, Nimble Brew, and Tremor on a ~30 sec CD that can be cast while the shaman is feared? If fears are so powerful, just nerf them and tone down the counters.
Mass Dispel and Shattering Throw have been around for ages and are not necessarily OP, but Divine Shield should be balanced around its own power. Make it reduce healing done by 50% and lower its CD to 3 min -- then make it immune to all dispels. Hand of Purity may not see much use because of the current flow of the game (and because Aff kinda sucks), but its design is flawed: an ability directly aimed at DoT specs and useless against everyone else.