The GC controller has just as many buttons as the PS2 controller, and I'd much rather have two large shoulder buttons than four tiny ones.
All your ideas just really say, "Make the GC controller just like the PS2 controller" and basically, the less it is like the PS2 controller the better.
Also, the fact that if you've really PLAYED any GC games, you'd see how un-important the D-Pad is, and how the positioning doesn't matter when you're rarely using it.
Don't complain about it being no good for fighting games either, that's what the graduated Analogue stick is for.