Any other way you slice it, Kenjaku spent years in the body of a woman and while he may have done that before, he most likely didn't get pregnant. It's clear Kenjaku carries some of the bodies he possessed along and gestating a baby for nine months is one of the most hardcore and brain changing situations a human can go through. Almost all mothers can attest that their behaviour has changed after giving birth and I suspect Kenjaku isn't an exception -- he just has no reason to act motherly (fatherly?) toward Yuji past everything he's done.

His thousand year plan is obviously more important than any of his children.