I still see good quality original N64 controllers fairly frequently at used game shops. I have at least 8, so I don't usually buy them unless it's a great deal or a cool color.
I would imagine that we'll see truly good replacement options when Nintendo decides that demand has risen high enough to re-release the N64 stuff as a mini classic or whatever they decide to do. I'm not super hopeful that it will happen anytime soon, though, given that many of the best N64 games are Rareware and Microsoft has the rights now. I think many casual fans would balk at the release of a mini N64 without Goldeneye, at the very least, and that's two licenses that I doubt Nintendo wants to purchase.
This discussion and my experiences at the recent con have made me think more about controllers and how tastes vary. For example, I've never owned a Neo Geo home console (AES), but, whenever I get the chance to play one, I'm left wondering what all the hype is about. The Neo Geo home arcade sticks may have been great for an era where no one could build their own Arcade Controls, but now they just suck. I'll never understand that stupid 4 buttons in a curved line layout. I loved the Neo Geo arcade cabinet, but it had quality commercial arcade joysticks and the buttons were laid out in a square pattern (at least on the one I played back in the day). The control pads for the Neo Geo got the button layout right, but I much prefer a traditional d-pad over the clicky thumbstick.
Similarly, people rave about the NES Advantage. I have two, but I keep them in storage because they're just not that great for most NES games. We knew this back in 1988. If you needed turbo, you were far better plugging an original controller into a 4 score.