Sure some instances wont be doable (occy, ToC, maybe not the last phase of HoR) but hell, I am bored as f*** and I wanna see how many instances that can be done.
Utgarde Pinnacle - Needs to pick up harpoons
Azjol-Nerub - Youll Never get it to go down the hole after the 2nd boss.
Ahn'kahet: The Old Kingdom - bots wont kill shadow copys,
Drak'Tharon Keep - Cant activate the alters
The Violet Hold - Cant hit the switches to down the water boss.
Gundrak - LastBoss - CC wont know what to do in skeleton form.
Halls of Stone - cant get to last boss.
Halls of Lightning - do able, if the profile is made correctly and toons are geared enough
The Oculus - impossible of course
Caverns of Time: Culling of Stratholme - wont run timed events. cant talk to arthas when needed to advance
Utgarde Keep - do able if geared correctly
The Nexus - wont get it to fall down the hole after tree boss, but doable if it back tracks. - Lastboss lots of dps needed to take down the dragon before the debuff takes your toons down.
so almost all of them have to have some kind of plugin or CC code for them to be done automatically. without user input.