Thirding True Sorcery.
Our group ran it in conjunction with the Iron Heroes classes and the mage had a blast coming up with custom spell effects. It is math heavy though, as has been mentioned, so prepping a few goto spells would probably be a good idea.
I will say that it was the one time as a player that I felt a "mystery to the magic" so to speak when spells went off. Of course this was a lower magic campaign, so it might not be your cup of tea.
As has also been said, limiting items/abilities that dramatically increase the Spellcraft check needed to pull of the spell-effects is a definite must. The stacking can get a little ridiculous with focci, components, taking extra time casting, etc.
All in all a solid system I feel.