I have seen something called Hori Mini controllers that were only released in Japan that look awesome. Main problem is that they go for so much on ebay lately.
The issue I have with stock N64 controllers is the trident design, forcing players to move their left hand from left to middle locations, sometimes within a gaming session. Talk about things that crash your game.
The Interact Super Pad 64 Plus controllers are an option that does not require switching hand positions in-game, but they are not symmetric in shape. This is where the Hori Mini Pads are nice. I believe they should have been the stock N64 controllers from the outset.