Institute flying - We have to many abilities that we can use to get around, the whistle alone is amazing. I hope they don't add flying until the end. I think it ruined a part of the game. That being said, it is a part of the game and will get added back so why not sooner the better.
World Quests - You are not supposed to do all the WQ, if you do then props to you but they are not mandatory to complete all of them, doing 4 world quests a day takes almost no time. Quick tip, if you don't have time to do them and it is a kirin tor or wardens, skip it and do it the next day or day after. You never have to rush these as you can double dip.
Artifact Power - this is fine, my alt has 20 on two weapons and 23 on another.
legendary - I agree that legendaries can be frustrating. They just need to fix them and increase the bad luck protection. I also don't like that an 860 ilvl item is better then my 895 ilvl.
BoA - Blood of sargeras have a vendor, the point of them are to be BoP. Artifact knowledge should not be BoA, the time decreases on alts, takes barely any time to catch up. What would the point of having reps BoA ? they are changing the arcway and CoS attunment so this isn't needed.
Only thing I really agree with are the legendary drop chance and utility sucks. but I don't want to change how you get them.