So many things they took out of the game that really made a difference and made it feel like a MMORPG. It started out really unique and had a ton of flavour. The class you picked mattered! They have spent the last 8 years making the game as easy to play as possible, without having to do a single thing yourself.
Most people will say PvP is the one that hurts PvE but it's the latter. Because of DPS and PvE they homogenized all specs so everyone can perform on the meters and what not. Look across the board on every ability and what every spec can do now. It's practically all the same so every spec can be competitive on the meters. Yeah, PvP sometimes has a negative effect on PvE, but PvE has literally destroyed the uniqueness of being a class and spec.
Also the fact they over simplify everything to make it more friendly to newer players which programmatically devastates the end game content. Look at Warriors on live now. What is it? 4 abilities to mash now?