In my honest opinion there are waaaaaay too many requirements to actually be able to make an upgraded City of Magic.They are as follows:
-Focal Point or Leyline
-Actually having that barony with a focal point or leyline be a free holding without cities/temples/castles
-The County must have at least 4 baronies because to be able to build a magic city the county must already have a city a castle and a temple

And since Focal points and leylines are quite rare this becomes even more rare.
The only exception to this rule is that when you convert to a magocracy your capital becomes a city of magic. So you could potentionally form a magocracy, attempt a coup and form a magogracy again but doing this for every barony that I want to be a city of magic is just tedious and not to mention i basically have to fight all of my vassals.

Suggestion: Make it possible to convert holdings in baronies that have focal points or Leylines into cities of magic via decision or something similar