If you want a flexible but dirt-freaking-simple magic system, consider taking the "Theory in Practice" stunt (from Science) as a baseline model. It lets you spend a fate point to use your Science skill for *any other skill*; if you do not succeed on your roll, you then take on a Minor Consequence as fallout for being wrong.
Basing this on Mysteries instead, you pretty much have your spell system right there. Spend a fate point, and use your Mysteries to do *anything* that you could conceivably do with another skill — even without having the equipment for that skill on hand (so, attack something at range with your Eldritch Bolts: that's the Guns skill, without its equipment). If you fail, however, you take a consequence — arcane backlash.
Combine that ability with several Rare Artifacts so you can pull more persistent magics out of your ass as needs be, and you're pretty much done. The core of this character is:
Mysteries - Superb
"Theory in Practice" for Mysteries
(one other stunt of your choosing)
Note: This is not mentioned above, but "Theory in Practice" has a prerequisite Stunt — Scientific Genius. In order for this rule to fairly emulate the functionality of Theory in Practice, the equivalent Mysteries Stunt (whatever you end up calling it) should require "Secrets of the Arcane" as a prerequisite Stunt.