Alright, here's the core idea:
Wizards, Clerics, and Druids do not get bonus spells from high ability scores. Instead, they get bonus spells per day from having ranks in a particular skill - Knowledge (Arcana) for Wizards, Knowledge (Religion) for Clerics, and Knowledge (Nature) for Druids.
How many do they get? Check half of their ranks in the appropriate skill, rounded up, against the bonus spells table.
Seems pretty simple, and you get roughly the same number of spells...