>>135617>N64 games that use both the D-pad and the analog stickPokemon Stadium (Pokemon Stadium 2 in JP) uses all three ways to hold the controller if you include the minigames, so if you want only one remapping for the entire game you probably want to map the control stick to both analog sticks, and two of the C buttons are going to have to be mapped to weird leftover buttons like R1/R2, Select, L3, or R3.
Tsumi to Batsu (Sin and Punishment) lets you aim the gun with either your right thumb or your left thumb while you use the D-pad or the C buttons to move around.
>BanjoBanjo has been brought over to newer consoles, so you could try loosely basing your remapping on the newer control schemes made for those.
https://strategywiki.org/wiki/Banjo-Kazooie/Moves