What I was trying to say (I'm not sure how clear this was) is that I think it's a good thing to wrestle with and not necessarily a good thing to have an answer to.
Let's think about it another way: O'Sensei was inventing something (sort of). His way was characterizing by many turnings and false starts and periods of questioning. Clearly, you aren't proposing that we each follow each of these steps in order to learn. It wouldn't really work even if we did. Or take another idea: O'Sensei's cultural heritage was far more militaristic and possibly more violent than that of many of us. Perhaps in this sense he had much further to go than the rest of us before he could realize some basic truths. Trying to 'put down the roots' you are thinking about may actually be more detrimental (in that it fosters violence) than it is helpful. I had the same sort of response to Paul Smith's comments. I think I've got plenty of Fudo-Myo all my own to wrestle with without 'goading' or 'cultivating' it.
Interestingly, I think these same issues come up in Buddhist and Zen thought. In my mind, the one thing that makes the way hardest is the need to give up on the notion that anyone can ever show you the way or that you will ever know the way. Similarly in AiKiDo, the hardest part is understanding that it is you who decides what roots you need and what roots you trust, and that you will never really know. All you can do is make sure they are truly your roots, and it seems likely that then will be as strong as they could ever possibly be.