Originally, the plan was naked Raiden’s privates could get exposed during combat

[PieToast]

I actually thought his privates weren't dangling around because they were tightly tucked in from the cold.

Maybe it was hard to render penises on 6th gen hardware, or maybe Kojima wanted us to mistake him for a women, because you know.... He was created to be the opposite of snake and to ridicule the male types that usually take the rule in those action movies and games MGS pays homage to.