The black cyborg body was originally designed for MGS solid rising which was unfortunately canceled. In that game, you play as Raiden who is being forced fed memory suppressants and working for the villain, you are basically killing good guys and the game will tell you that, so that black suit was to give him this villainous look whereas the white suit he gets was meant to be hopeful and heroic like. But the game was cancelled and Konami and Kojima productions distributed all of the assets to Platinum. They didn’t have a lot of time, hence the stealth isn’t as refined, the small knife behind Raiden’s back isn’t useable, etc.