The origin has nothing to do with film structure. It has to do with story. So that's like saying the story of ESB is different than ANH because it is. Though I will agree the structure of linear/non linear is different. I said there were differences, but there are many similarities. Though the positive note, and themes again is story. ESB is darker then ANH. Just story choices, nothing to do with structure.
Though the non-linear aspect and linear aspect yes I agree on that. Though originaly the script of BB had it linear, and later they must have decided differently.
Irregardless, I doubt its going to be "Pulp Fiction" is my point. It is not going to be radically different from that of Begins and TDK. Will he go back to the way of BB? In terms of structure maybe, but I doubt the story will focus on tons of people ala Pulp Fiction then combine together is the point.
EDIT: And as well I just never felt that TDK and BB were that different in terms of many things due to the fact the same character and "actors" for the most part, and they seemed to bridge the gap for me. It was a continuation of themes and ideas from Begins and at the same times yes trying new things. To me they felt like of one series, but of course visually and some of the structure was different. Yet BB at the last half was linear.