Clearly Itagaki didn't have access to the original engineering team he worked with at Tecmo, but in a case like this, I feel simply iterating on the technical work from Ninja Gaiden would have helped a lot. UE3 is a bad choice for Wii U and Japanese development studios don't have a great rep for using it well.
From what I understand, the switch to UE3 happened soon before the Nintendo E3 reveal. It was running on Vigil's Darksiders tech before that, AFAIK.