LOL, found New Rules after posting to Skills and Magic.
Here's an idea I've kicked around as a homebrew ever since 3rd Edition.
Split out the Spellcraft skill into the different schools of magic, much like the Knowledge, Profession, Craft and Perform skills.
Spellcraft (abjuration) (Charisma-based, Trained)
Spellcraft (conjuration) (Wisdom-based, Trained)
Spellcraft (divination) (Wisdom-based, Trained)
Spellcraft (enchantment) (Charisma-based, Trained)
Spellcraft (evocation) (Intelligence-based, Trained)
Spellcraft (illusion) (Charisma-based, Trained)
Spellcraft (necromancy) (Wisdom-based, Trained)
Spellcraft (transmutation) (Intelligence-based, Trained)
Spellcraft (universal) (Intelligence-based, Trained)
Now, you're asking a lot of why's and how's probably. Here's some of the proposed changes:
First off, you'll need to give spellcasters more skill points. Probably give the heavy hitters like Clerics, Druids, Sorcerers and Spellcasters another 4. I wouldn't increase the skill points of the Bard, Paladin or Ranger, since they aren't primary magic-users, but rather dabblers in the art.
Okay, now for the real overhaul part. Change the Magic system. No more spells/day, but rather have them roll a spellcraft check every time the magic-user wants to cast a spell. Now you might be seeing where the different ability modifiers for the schools comes in. Bards & Sorcerers would excel at Abjuration, Enchantment and Illusion spells, Clerics & Druids would be great at Conjuration, Divination and Necromantic spells. And Wizards would be the Evocation, Transmutation and Universal go-to guys.
Beautiful part is, we don't have to change the spells themselves, just how we're using them.
To cast a spell, you have to succeed at a Spellcraft check of 10 + 2*Spell Level (so a 0 level spell is a DC 10, a 4th is DC 18, a 9th is DC 28). If you succeed, the result of the check is the Saving Throw DC that the target has to overcome (makes the lower-level spells more powerful, keeps the higher level in check). If you want to Metamagic the spell, increase it's level as noted in the metamagic ability and calculate the new skill DC.
Bards and Sorcerers still only known a certain number of spells to cast from. Divine casters make the Spellcraft check, basically asking their deity for the spell. Wizards get a mod. They know a certain number of spells like a Sorcerer, but they can have extra spells in their spellbook that they can cast as long as they use their book. asting a spell that usually takes less than a full round while using the book increases the casting time to a full round. But using the spellbook gives a +5 insight bonus on the spellcraft check since you're following the 'recipe'.
The last part is what keeps everyone honest about the spells they cast. I borrowed it from Shadowrun's Drain rules, and modified it for use with this. Basically, when you cast a spell, if you succeed the check by more than 5, nothing happens. If you succeed by 5 or less, then you take that number as nonlethal damage. So, if the Spellcraft DC is 18 and you get 21, you'll take 3 nonlethal damage. if you fail the check by less than 5, then you'll take double nonlethal damage and become fatigued (i.e. DC of 18 and you rolled up 15, then you'll take 6 nonlethal damage). If you fail by more than five, then the difference becomes lethal damage.
So, any ideas? Suggestions? Flames?