So we've seen that there are other schools of magic out there- PigsWick, DragonSpyre academy. So what if there was one giant school atop a huge floating island where all of the best students from each magic school congregate together and learn highly advanced versions of their magic types. Each school would have it's own dungeon, and after you beat the dungeon the Master of the school decides you're worthy to learn there.
On a slightly more advanced note: Khrysalis should turn out to be where the old Shadow Dungeon was located, but then it was broken away by Morganthe in some fit of rage or act of spite when she was expelled from the school for unruly conduct. Little pieces of it remain, four section of the main dungeon, each one you must go through to learn the secrets of advanced Shadow Magic.
I mainly had this idea because sometimes you really wish you could keep using your second school, but they just seem so weak compared to your school spells. I guess you could imagine this place as a wizarding college, with the best teachers, students, and spells from across the spiral. The new wizarding upgrade could be Penultimate (penultimate necromancer, penultimate pyromancer, etc.), and the new spells, while costing plenty of pips, would also be stronger.