Heh...in my opinion, every one of your reasons given here are reasons this SHOULD be a separate power source with separate classes.
Rock Lee, Sasuke, Naruto, Yaruka, Gara, Kakashi, et al all use Chakra to power their abilities but they do so differently. As you pointed out there are three main categories: Genjutsu (Defender), Taijusu (Striker), and Ninjitsu (Controller). The important factor is that the guy with the bugs (whose name always escapes me) could render any of them powerless with his chakra eating bugs. They are not using different power sources.
Honestly, I would be LESS likely to allow a class that hybridizes not only 3 power sources but three roles than to allow a well though out concept for a new power source with appropriate and balanced classes.
I think that proceeding the way you are is, honestly, folly and will lead to a balance nightmare that few DMs will want to take the time to wade through.
YMMV
DC