Alright, so I've recently been... digesting... Chuubo's Marvelous Wish-Granting Engine (I have a MA in Borgstromancy and Ars Morani).
One of the interesting things about it are the Miraculous Arcs, which work... kinda like classes. You even multiclass them in a way that's pretty similar to 3.5!
Now, here are two nuances that I could see extracting and applying to a different system.
1) Each Miraculous Arc gives you a power that you only have while following that Arc. Swap Arcs, and you switch it for the power your other Arc gives you.
2) Arcs function over the "level", rather than at the end of it. You start at a rating of 0 in one Arc; gain a "level", add 1 to your rating, and then you can either pick to continue with an Arc you've already begun or start a new one at 0. This is a really fine distinction, but one that combines with 1 to give... interesting results.
It's like... I dunno, imagine that the Wizard gave you the "Arc Power" of learning new spells, and the Fighter gave you the "Arc Power" of picking up new fightin' moves.
You start out at Fighter 0 - you get whatever basic Fighter powers you might want, and then can learn new fightin' moves!
You complete that level, and are now a Fighter 1.
If you want to become a Wizard, you become a Fighter 1/Wizard 0, who can learn new spells.
Your Fighter 1/Wizard 0 can't learn new fightin' moves - that's not what they're focusing on at the moment! If they were, they'd be aiming for a new level of Fighter.
And so on and so forth. It works more smoothly in Chuubo's, since the classes are pretty general... but it's an interesting way to look at stuff.