This is something I have been thinking about for years and I think I have finally had the inspiration for a perfect compromise.
A non-spontaneous caster must focus their mind each day by study and concentration or prayer with the engergy/mindset needed to cast spells of a certain power (level) and school of magic.
For example, a third level caster prepairs:
1 Second Level spell: A Conjuration spell (for example)--lost when cast
2 First Level spells: A Evocation spell, a Transmutation Spell (could have been two evocation)
4 Zero Level spells: Pick 4 schools that can be cast at will.
The exact spell from the prepaired school is chosen at casting time.
This is still compatable with Pathfinder specialization benefits (is an oppositon school prepaired that day? If so, benefit lost).
Depending on how you handle metamagic, you could require a spot reserved for a quickened illusion or example (although not all spells of that type may benefit), or be more strict and require the exact modified spell be used in the slot (this keeps metamagic more adventageous for spontanous casters).
You could allow a specialist wizard to use any spell type for a spell of their specialty, but I think this is too powerful vs. spontanous casters, and universalists.
Unrelated, but it might make progression more uniform and reasonable, would be for the Cleric to choose one domain as primary. The only impact is that the 4th, 8th, 12th, etc. level abilities come at 3rd, 5th, 11th, etc. This makes more level increases "interesing" and prevents other from being such large jumps in power.