Chakra System

I believe Naruto Forum Rp has something similar to what you're recommending. Perhaps take a look at it. It's an entire classing system used to determine one's strengths and focuses. Including limits much like the one you're describing.

I never really got the just of the whole system myself, but I believe we could use a water downed version of it with relative success.

Off-topic:

Hmmm. I agree that over complicated systems like this could really limit RPing. But yeah I like the sound of limitation on jutsus or something, jutsu usage has been utterly abused in this site for a very very long time.