Good points. It might be time for recount and other DPS meters start factoring in the "effective DPS" each time a HoT or bubble is dispelled, and fold that in with "damage done" or next to it by default.
I haven't played my hunter recently but last I tried after the draenor changes, I felt like too much was stripped away. BM is my favorite spec, whether it's OP or not, and MM is my least favorite. Blizzard seems to have a very lax approach to pvp in this game. I mean, look at ashran, it's basically a raid with "pockets of pvp" tossed in. It's hardly a pvp zone when the only way to progress is to overcome pve objectives.
I don't know why they changed bestial wrath. It was fine the way it was, acting as a trinket. Made the BM spec unique and a force to be reckoned with...I had a lot of fun as BM in MoP.
I keep my pet on passive and have macros that force the pet to attack the target I am focusing on. It's not a DPS loss, especially if you go with blink strikes...a must-have talent for BM in my opinion. It's more of a DPS loss if you rely on the sketchy "pet assist" AI.