There are a couple of different issues at work here, I'll try to touch on what I think are the most important:
1. Blizz can't, or doesn't care to, make PvP keep up with PvE.
The game is made with PvE in mind, and PvP is merely an afterthought. Changes to PvE, i.e. balancing the damage/healing meter race as well as the introduction of "fun [sic]" new legendaries, trinkets etc. constantly deal crippling blows to the already pitiful efforts made to keep PvP from spiraling out of control entirely.
2. No functioning interrupt system
This is why simply reducing damage by x% won't solve the problem. It would just make healers too strong. Since the interrupt system in WoW is based on cooldowns (school lock, silence), you get a certain time frame in which you can kill your target (e.g. when you just successfully locked a healer out of their healing school) or, vice versa, a certain time frame in which you can get your target back up (e.g. in between lock-outs). Another attempt at solving this was to inflate the amount of health players have, which Blizz tried and failed to do with Cataclysm. But if they had succeeded it would just have resulted in another kind of arms race, DPS vs. HPS, i.e. dicking around until the healers run out of mana.
3. Too much crowd control
This is the primary reason why PvP gets worse with every expansion. Blizz just keeps adding more and more abilities. The game has too many different types of CC (resulting in CC-Chains) and most of them are too easy to apply and too hard to counter; plus there's the horrible system of Diminishing Returns which allows people to chain the exact same kind of CC.
4. Instanced boxed PvP
This is the magnifying glass. Aside from it being lazy and bad design, as well as a tremendous disservice to actual PvP, it also exacerbates existing problems. By stuffing PvP into a box even slight balancing issues become immediately noticeable, like potholes in a car with broken dampers.