For starters, I'll just agree with
@jobo (don't get used to it!) that if kickboxing interests you, it's a good next move. I'd say much the same about almost any MA you were interested in, because your personal interest will carry you through frustration and boredom.
That said, let's also look at a generic person (not necessarily you) looking to add to their Bujinkan training. From what I understand, many Bujinkan places don't do much working against a resisting opponent, so anything that gives you some of that will be a great compliment. If it were me, I'd be looking for significant striking (kickboxing, as you said, will give you that) and something to expand the utility of the grappling (some BJJ, Judo, catch wrestling, etc.) by working with folks who are actually trying to stop you.