Hardo, this is strange, I also spent the day testing MoP dungeons, only did Heroics, but my results are not exactly the same as yours. Most peculiar is the fact that you can do Temple of the Jade serpent, where Mesh issues hinders me from even starting the place. Other than that, yes, quests can cause problems, both when bots are waiting to pick em up. but also when they need to turn in, but aren't doing so.
Shado Pan Monastary - Sha of Violence is still the hardest fight in here, but seems fully afkable
Gate of the setting sun - Fully afkable.
Scarlet Halls - Toons get caught in Armsmaster Harlans Blades of light, had to manually guide em past this encounter. Not fully afkable atm.
Temple of the Jade Serpent - Mesh issues, not possible to run at all. (unless you drive the tank manually)
Mogu'Shan Temple - Harder than I remember, And I think Hardo is right about the Trial of the Kings, I remember I was loosing aggro here alot, but never realised the Tank stopped fighting.
Siege of Niuzao Temple - The toons are not good enough at tossing bombs at the reinforcements during General Pa'valak fight , this leads to tons of adds and alot of wiping, eventually they might bruteforcing this encounter, but I usually turn of one bot and run him manually to toss bombs at reinforcments. Afkable, but painful.
Scolomance - Fully Afkable, Harsh lesson can be annpying though, and pulling the room with bored studens ofter results in a few wipes since the tank really wants to pull the back up the stairs while the dps doesnt care and do full out dps and getting aggro.
Scarlet Monastary - There is a mesh issue that prevents my toons to go from the corridor into the second courtyard. As Phelan said, the tank also pulls all the mobs in here at on, making this fight tough....
The Brewery - Fully AFKable
This is what I remember from today
Edit: After thinking about the differances between mine and Hardo's result I went back and deleted my Honorbuddymeshes again, and voila, now it seems like Temple of the Jade serpent is working.