IMO they should take the following things from each addon:
Classic: Class identity. Healthstones should heal more than potions, Non-Healing Druid specs should have healing cooldowns like Tranquility and such stuff. Removing class identity does not prevent class stacking as long as damage numbers are noticable different and abilities like cloak of shadows, iceblock, and other immunities exist. The gear and ilvl scaling. +/- 5 main stat should matter, not having +/- 500...
BC: The difficulty of dungeons. Using CC and controlled focus damage needs to come back (more!).
WotLK: The athmosphere.
Cataclysm: -
MoP: The storytelling, raid difficulties and sizes, fixed 20 man for mythics doesnt worked out as it was promised. The PvP system (stat templates and pvp templates aren't working well either).
WoD: Garrisons. WTF? Yes, but inside the main city hub and for guilds to build. With consequent updates and expansions, and better inclusion into the story
Legion: World quests but less of them (more like daily/weekly). Make them interesting and not a grind fest. It is like always: the least challanging content has the worst rewards, and to keep it relevant it gets grindy. The gearing system, but with reduced margins. Having always the chance for an improvement is great, but not if you have to be so superlucky to upgrade 50+ itemlevels.
What to remove:
Group finder, LFR, artifacts, legiondaries, the lead game designer.