One thing that is missing in most fantasy games is the concept of Black Magic vs. White Magic. I think it would be interesting if players were only able to use White Magic (heals, blesses, even holy fire), but Black Magic would be NPC-only. Stuff like zombie creation, curses, and magical diseases would not be available to players at all (or they would be heavily penalized for using it).
Older D&D sorta does this, with reversible cleric spells, but it has no implications if your player uses these spells (other than clerics possibly losing access to magic, but no issue for mages).
The best version I've seen of the split between White and Black magic is the various Star Wars games. Seriously. The various mechanics for turning to the Dark Side would be a fantastic baseline for a fantasy rpg. Instead, games tend towards the cthulhuesque penalty (a la Dungeon Crawl Classics), if they have any penalty at all.