The dark side eye colour is the same as " dark side corruption makes you ugly" - it's just a game thing.
I agree that both are silly.
In Episode III, Anakin's / Vader's eyes changed colour outside the Jedi Temple and then went back to their normal colour; the Emperor's features became ugly as a result of the force lightning bouncing back at him. In Episode VI when Vader's mask is removed, all we see are scars from his duel with Kenobi, nothing more.