Unlike the standard Nintendo 64 controllers, these prototypes (black / gray) have a "smaller shoulder, longer handles, a tiny bottom trigger, Ultra 64 decal slot, bigger and more delicate analog stick, flat non rounded buttons, and a round axis indentation for analog." Video after the break.
As you can see, it's not radically different from what the Nintendo 64 controllers eventually became, but interesting nonetheless, especially when you look at the stick design - thicker and thicker in each iteration[via GoNintendo - Insertcredit]
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[Source: Tech Blog]