The N64 controller wasn't as dumb as everyone thinks it is when you realize they designed it to play both 3D games and 2D games in an era where 3D games hadn't been out long, so they didn't really implement using the D-pad for other inputs yet. They intended the thumbstick for 3D, and the D-pad for 2D. Obviously now we know that it's useful to have the D-pad mapped to secondary functions, which is why people think it looks weird.
Commenter in the other thread already nailed it, lots of companies put some thought into ergonomics before the PS1 controller.
The PS1 controller was just the first one to sell enough that everyone had seen one since the boxy NES controller.
The N64 controller wasn't as dumb as everyone thinks it is when you realize they designed it to play both 3D games and 2D games in an era where 3D games hadn't been out long, so they didn't really implement using the D-pad for other inputs yet. They intended the thumbstick for 3D, and the D-pad for 2D. Obviously now we know that it's useful to have the D-pad mapped to secondary functions, which is why people think it looks weird.