Couldn't you just swap the wires from where they connect to each button to the more convenient button?
See...why didn't I think of that. Listen to this man, and not me. This method is much easier.
Well there aren't actually any wires to swap, since the buttons are mounted to the PCB's. I actually did rearrange my DOA4 stick's buttons to the more standard layout of:
X:Y:L
A:B:R
What I did was take all the buttons off the PCB, and then just ran wires to all the contacts.
Be warned that the desoldering of the buttons isn't the easiest thing in the world to do though, especially if you have no experience with such.
[EDIT]
Actually... There were wires that could be swapped.
The controller has 3 PCB's. One for the buttons up top, and then 2 for the main buttons. One of the ones for the main buttons was just a button PCB, and that one is able to just have its connecting wires swapped.
It has been a long time since I modded mine, but if memory serves it was only 2 of the six buttons that actually required desoldering from the PCB (A and I think B).