Bah, personally, I believe the best alternate magic system out there is the Sovereign Stone magic system... but then again, I am completely and utterly biased
Instead of the slot and cast spell system, Sovereign Stone uses a Casting Threshold. You learn certain spells as Intimate Knowledge, Quick Reference or Full Reference. Each spell has a casting threshold, the higher the threshold the more difficult the spell. Each round, the spellcaster rolls 1d20 and adds modifiers in order to equal or surpass the casting threshold, at which point the spell goes off. The magic is elemental based, but each element has specific aspects that pretty much cover the spectrum: Earth has healing and construction, Fire has conversion and divination (past), Water has communication and divination (present), and Air has mentalism and illusion, in addition to their elemental aspect. There is also the Void, which is the necromantic/shadow magic that can also mimic the destructive aspects of other elemental magics. It's easier to use, but more dangerous at the same time.
Yes, spells are a bit more difficult to cast, and there is always the chance of being fatigued (or worse) by the casting, but the spells can be quite powerful.
The initial system is contained in the Campaign Setting, but in our Codex Mysterium, our magic sourcebook, you find complete rules for creating magic items, creating new spells, and more than a hundred new spells, along with the basic rules for spellcasting. The only things not contained within the book is the information on Spellcraft, the Detect and Dispel versions of the magic, and a large selection of basic spells.
If ya have any questions, just give me a holler, I'm more than happy to help.
- Christopher