It may be interesting to have a form of very powerful and rare magic ("High/Forbidden/Dark") that is balanced by hefty consequence. Such as mandatory sacrifice (of a companion, magic items), permanent (or semi-permanent) penalty, or having certain factions/companions react hostily. Something like this would likely need to be written into the story, not just as a general mechanic.
Another idea would be adding a risk vs. reward system to magic, such as empowering spells with a chance of backfire.
In general I like my magic flavored with mystery, unpredicability, and a sense of meddling with dangerous powers not meant for the weak of will.