Really the only two things I'd want are
A. switch the select and B buttons (to more closely mimic LSDJ)
B. do away with the transport screen in favor of a screen map ala LSDJUnfortunately, from my correspondence with Neil I don't think either are an easy fix.
I kind of felt the same way when I first started messing around with the program but now that I've been using it for a little more than a week the navigation doesn't bother me anymore.