I've participated in some seminars held by Genbukan and Bujinkan dojos. As much as I could understand and see, they essentially teach the same things but are lead by two different people (that used to be friends or something). Some say that Genbukan is more strict in adhering to the tradition while Bujinkan seems to be more "flexible" about it. The people I met were quite good at what they were doing so I couldn't really see a big difference. Whatever the heritage, it's always the quality of the teacher that really matters.
As far as the relation to the traditional jujutsu goes, they do follow the older method of teaching based on kata, predetermined attack-defense matrix, practice on hard surface and some ceremonial you don't usually see in modern schools. It suits the application of their techniques which are hard and painful since the use of join locks and pressure points/strikes is a common feat. For the same reason there is no competition-based practice. They also practice with traditional weapons such as katana (boken), bo, knife or so but I'm not familiar how it actually fits in the overall system. They adopted the modern belt-ranking system to mark student's progress.
From a judo or modern jujutsu perspective, their teaching is valuable both from the self-defense and cross-reference aspect. In my view, judo masters should at least get familiar with it (or any other traditional school) if they want to fully understand judo. For comparison, I was positively surprised that both Genbukan and Bujinkan masters were quite familiar with modern martial arts. Still, the kata-based methodology and use of brutal (aka "traditional") techniques has its drawbacks and from what I could see such dojos have a smaller number of students. Once I participated in a 3-day Genbukan seminar and ended up with a number of bruises and a strained elbow. It was an extremely valuable learning about self-defense, but I cannot see myself doing it all the time. Of course, it all depends on personal preferences and positive feedback.
I hope this helps.