I don't know much but what I do know I'll speak of.
Genbukan is supposed to be a more traditional style of ninjutsu than Bujinkan is. For example, Bujinkan adds in some up to date flare. So that it can keep up with the times. Genbukan doesn't use that a goes purely traditional. How traditional is a good question. One that I can not answer.
Jinenkan is like Bujinkan but is focused on the basics. They believe if you have mastered the basics then you can master everything.