If one is doing the kata properly then the movements (the techniques) are not being neglected. Use of the movements (application) is neglected because the practitioner usually isn't taught how to view, experiment, and use them.
I tend to use a lot of drills that use movements from specific parts of katas/forms and require students to find and show where the techniques are within the kata/form. Once students can do that out of a specific drill they must then find for themselves a different application for the same technique/s.
Interesting stuff. A couple of things I wonder about ...
1) The directionality principle is rather less than obvious from just viewing the kata, because the actual footwork in the kata doesn't match the proposed principle. He says that "a technique on the right side ... indicates that you orient yourself so your opponent is on your right side." In the bunkai, he demonstrates that point with angular footwork and body shifting. However the kata itself doesn't include that angular footwork and body shifting. To my mind the footwork is more important than the movement of the arms. Why would the designer(s) of the kata leave the most important element of the techniques out of the actual movement and hide it in a way that you need the code to understand? Did they not view the footwork as being so important or were they deliberately trying to hide the meaning of the kata from the uninitiated?
2) He shows several "what-if" trapping sequences built into the kata for when the opponent blocks your first strike. What he doesn't show is how it works when you are unable to grab the wrist of your attacker's punching arm. In my experience, catching an attackers punch is the hard part. The rest of the trapping stuff is much easier in comparison. Theoretically you can initiate the trapping sequences off of your opponent's block, but it's a lot trickier when you don't already have his other hand controlled. He can either back away or hit you with the free hand while you are trying to trap his blocking arm. Does the kata have elements to address the situation where you are unable to grab the punching arm? The proposed bunkai all seem to presuppose being able to get that control.