England didn't conquer Scotland but they certainly tried, France as well. The vanilla victory conditions were lame (hold 50 regions plus Jerusalem, how interesting!) but maybe letting the player follow the factions overall goals would be less strict.
Good news about the increase in popey harshness though! Be really hard to expand if you're surrounded by Catholics.
You're right about it being probably not worth England attacking Scotland. It would have been a major headache for not much cash I imagine.