I'd just have all the characters of a given level be of the same refresh. I wouldn't try to limit refresh for wizards. Maybe just balance their skills and powers more. That's easy enough. You can keep wizard templates in line by limiting how many refinements they get. Make them more interesting by giving them powers instead. So instead of giving 2 extra refinements, give a "transporter" type wizard World-walking.
Especially with Pathfinder Sorcerers and blood-lines.
[thinking out loud] If you're going to try to do spells/day, I think the easiest way would be to use specialization pyramids. They already exist in the game, so it wouldn't be too far from existing rules.
I'm not sure what you'd base it on, though. Flexible spell-casting is what makes the magic system cool. Maybe just have it as-is (where you can get roughly 4 or 5 spells in a single combat) but have bonus castings based on your refresh level...
[/thinking out loud]
I think the easiest way to set the whole thing up is to do a base template for each "class" at minimum refresh then a base template at the highest refresh.
At the highest refresh, you can indicate at what refresh level they acquire new powers. Just list the powers in the order they get them.
The more complicated thing will be doing individual skill trees (which you'll probably have to build from the bottom up) and, for casters, enchanted items.
