Re: Naruto
Yeah, the chakra element explanation is relatively recent in the manga, and we almost got an explanation for how Shikamaru and Chouji's jutsu work.
Also, you might want to considdering adding a fourth skill called Chakra Control for those jutsu that aren't typically involved with the other types, namely things like water walking, wall walking, super strength, healing, and even rasengan.
Another good way for them to get alot of jutsu easily is to use a cost divider, like 3 or 5. The VPP to me seems a little powerful, and generally fits with Sharingan better, though I'd also model Gaara's sand with it since it's being given to him by that nasty little demon inside him, though you could just do that with typical jutsu and just say he learned it from shukaku.