Even the analog stick's issues for the N64 I'm pretty sure are just a case of 1st generation unrefined-ness. As for not being able to use Z and L, again, that's just an issue where the idea of just putting two analog sticks on both sides had never been considered, and coming from the SNES it wasn't seen that there'd be a reason to actually need two shoulder buttons per side considering the Z button just essentially replaced which ever shoulder button was unreachable.
Also the original GBA doesn't get enough love for it's awesome ergonomics (for a handheld anyway).
I have small hands (internet research says my hands are average female size...but I'm a guy) and I find the 360 controller ergonomically very comfortable as well - the only other two I find as comfortable ergonomically are the GameCube controller and the original "Duke" Xbox controller - yes I realize I'm probably the only person in the world with small hands to actually like the Duke controller. Note that the backside of the triggers on the Xbox's S-controller bumps against my middle fingers, my guess being because my small hands don't have a large enough gap between my index fingers and middle fingers. Also I've never really used the dpad on the original Xbox controller, so I left it out of my previous "crappy dpad" controller list.
ANYWAY...
-Will the Wii version SUPPORT Memory Cards as well? I already have 3 memory cards I can use and I can't trust NMM yet.
Has not been confirmed nor denied but considering even normal Wii homebrew can read from GC memory cards (see GCMM) I can't see why this wouldn't be implemented...
-Will the Wii version support NGC controllers? I feel most comfortable using those.
The Wii version, as of what has been currently announced, will ONLY support GC pads.
-Will the Wii U version support Gamepad Pro or just the regular Gamepad?
As of right now neither - it currently only supports USB controllers.
-Why is there two versions one for SD and one for USB? Wouldn't it be easier to just have one version for each console?
We had this discussion earlier and the conclusion is we came up with is "that's how crediar decided to do it"
-Are there any plans for adding Quadforce too?
I cannot comment on Quadforce since I do not follow its development and therefore I've no idea if crediar has said anything regarding it at all or not.
-Will there be a frame patch like Devo?
Do you mean the widescreen hack? If so then yes, in fact it's already been demonstrated on crediar's YouTube channel.
-Wouldn't it be awesome if the Wii U version used the gamepad screen to emulate a GBA link cable? How difficult would that be if I may ask?
Considering Nintendon't at least currently only supports GC pads and USB controllers, you'd probably have better luck finding such a feature in Devolution.