I think adding on a second analog stick to the N64 controller is useless since the games were programmed having one joystick and 4 digital C buttons. Its like using the 3DS's circle pad while playing a DS game. Sure you're using an analog stick, but the input to the game is still digital, it makes absolutely 0 difference.
I don't have a problem with n64 controllers, except the deterioration of the analog stick. I blame Mario Party for that. I have one shitty controller for mario party style games, and 2 controllers with very good joysticks for stuff like Goldeneye. In games like Dr. Mario 64, I think the D-Pad is a must. There is no way that you are using a joystick for that. I don't think there is much improvement to be had using a second anolog stick on 3rd person action games, which from what I've seen is most of the n64 library anyway.
That problem isn't exclusive to the N64, other controllers have deteriorating joysticks too. Have you been to a Walmart or McDonalds lately? every controller hooked up to a demo unit is pretty much fucked up. My Game Boy Color's rubber buttons have worn down since I used to play it so much (need to find a broken GBC so I can replace those rubber things).