I believe I have had the experience and pleasure of knowing you long enough to know that when you ask a question it is not to cause problems.
To oversimplify, the ninjutsu teachings seem to be about how a practitioner can make themselves powerful and effective. Basically it is "what can I do to him (the opponent)?"
Aiki principles go to the other end and look at what is going on outside of the self. I.E. "What is he doing that will thwart himself?"
It was my teachers' opinions that aikijujutsu training and ninpo taijutsu training were both effective but at different things. aiki techniques show how to use an opponents energy against him, while the ninjutsu side (and the samurai arts taught along with it) teaches you how to make your own attacks more effective.
Here's two similar inner wrist twists from an aikidoka and a practitioner of BBT. Keep in mind that I have respect for the practitioners of all arts and I chose these clips for the sole purpose of them being short and the best I could find to compare why we view each organization to be lacking in what we were striving for.
Bujinkan
Notice how once he seized the wrist his partner stopped attacking him? Throwing one punch and stopping does not seem realistic to practitioners of aikininjutsu. Even from a teaching standpoint the technique should flow as if it were a real fight, which this technique does not.
aiki
This energy displays more closely the type of attack we are looking for where the uke continues to move towards you after he strikes. What is not seen here that is in aikininjutsu is that we will strike at targets while performing this technique using methods found in the takamatsuden arts.
We will be releasing vidoes shortly so hopefully I can show you a 3 way comparison between how those two do a wrist lock and how we choose to combine their methods to the greatest degree we can comprehend.