I would consider turning off prepared spells for Wizards.
Sorcerers & Bards have access to a list of spells and may cast any of their 'known' spells.
Wizards have access to the same spell list as Sorcerers and may cast any of their 'prepared' spells.
What many, many, many players & DM gloss over is the cost of creating & maintaining a magical library.
Adding a spell to a spell book takes 1 page per spell level & 100 gp per page.
It costs even more if spells are copied from a library or friendly wizard.
Wizard characters have limited resources same as all other classes.
Here's a quick comparison of the costs to fill a spell book with all PHB spells vs. approximate character wealth at those levels:
- 1st level - 58 pages 0 & 1st level 5800 gp vs. 100 gp
- 3rd level - 100 pages 2nd level 15800 gp vs. 2700 gp
- 5th level - 126 pages 3rd level 28400 gp vs. 9000 gp
- 7th level - 164 pages 4th level 44800 gp vs. 19000 gp
As you can see, unless you also suspend character wealth guidelines, your wizard will never have the resources to author a complete spell book.
After costs, wizards need to account for the bulk and mass of spell books.
Unless you suspend rules and let the wizard cast without the book at all, he will be limited to the spells in the book he's holding.
In the above example, by 7th level that wizard is lugging around 5 spell books.
At 3 lbs a piece that is 15 lbs of books, about half the carrying capacity of an average STR individual.
Switching books in combat will be unwieldy, so you're back to keeping track of what spells are written in a particular book vs. what spells are prepared.
This creates a parallel to the OOC problem with allowing full access to all spells without preparation.
Spell descriptions are spread over a dozen books, at least in 3/3.5 edition.
If you waited for a player to research exactly what spell she wants to cast in any given situation, the game grinds to a halt.
Just as combat doesn't wait for a wizard to read through all his books to find the right page, a playing group won't wait for the wizard player to do the same.
Prepared spells lists really do serve a game flow purpose, as well as a game balance purpose.
For Clerics, I would consider letting them go off-list. However, I would subject them to the same cost-constraints as the Wizard above.
Conclusion-- the game is balanced pretty well as is, just consider the player anticipation over what spells to prepare to be part of the fun.
