Although I'm just begging for the legions of purists to cry havoc, my honest thought is that the best way to overcome the wearing down stick debacle is to use replacements that are durable and good quality, then just adapt them (n64-n64 or n64-gc) a la whyieyesya's standard ones to correct for the poor control stick mapping.
IE: I use this stick for smash64 because the hypersensitivity isn't a problem for that game (in some cases it's useful):
http://www.amazon.com/Redesigned-REPLACEMENT-Joystick-Controller-Thumbstick/dp/B009MRZAUC/ref=sr_1_1?ie=UTF8&qid=1437259168&sr=8-1&keywords=n64+replacement+stick
It's good quality, hasn't gotten loose, and feels like a gamecube stick. Why not just adapt the mapping of this stick or a similar one to match the original mapping?
I have a few of those lying here (was able to get 4 of them for about 10$, so it was a great deal, obviously the guy wanted to get rid of these shitty replacement sticks). I am not sure if they can be fixed this way. One thing I noticed is that the sticks have a huge amount of lag. When I tried to do a side hop with sword out, Link would just do a jump slash. I actually had to push left/right slightly before pushing A, to do a sidehop. That is how bad the lag is. There is a small chip inside the analog stick that is checking the analog sticks value. Apparently that is done too slow and it can not be fixed with an external adapter. Furthermore, the deadzone might be a case where there is no output noticeable from the analog stick for a long time, in that case an external adapter would not help either.
I can totally give it a try though, perhaps the deadzone issue can be fixed this way. One thing I am afraid of though is that there is a lot of differences between these sticks. I actually also read about people not having any problems with these sticks. Perhaps they do not notice. Perhaps there are different versions out there.
There is a guy selling a custom PCB that goes inside the replacement stick. It resolves all these issues. I believe he sells it for 10$. You do need to solder I think and you also need to somehow open the stick's case, since it is glued..
One more thing, I am not sure I really like these GC style sticks. Imo, the N64 analog stick gives you very precise control. It is very easy to hold ess in place.
Maybe we need to find someone who is really good with 3D printing, although I am not sure if we can make strong enough parts with that.. If only we could get the mold that Nintendo used..