No Sarthaal amulet (you need Tolfdir's permission to enter)
Impossible to become Archmage
Won't get to fight the dragonpriest (to get his mask)
And that's off the top of my head. If there is a way to fix this (barring reloading my last manual save because the autosave system svcks), please let me know. Otherwise, please work this in your next patch.