The original case is huge. Without trimming the board at all, you can make a portable much smaller than the original case.
if you really want a small portable, RCP wiring is a viable alternative, but it isnt easy to do. matter of fact, its just about the smallest dot pitch you can find on any portable project. Dont try it unless:
A) you dont mind killing every n64 you touch
B) Are very good at soldering.
Now, I know you dont have to be a god to RCP wire, but its not something someone who has never soldered before can just pick up and do.