I'm one of the few that liked the GI Joe line... although I'd have preferred more card-art accuracy, what I did like was that they were relatively consistent across the line. Because of that consistency, they look great on the shelf!
For me, that's the problem with this Punisher. If he's already got bright white boots and gloves, there is no reason for the Skull to be faded.
As others have suggested, this would be better done similar to the DC Batman. Do one version of the figure with white gloves, boots, a bright white skull, white magazine pouches at the front of his belt, in other words, a more comic version. Then do another version, more tactical, military, with a faded skull, black/grey gloves and boots etc.
I wouldn't mind if he didn't have a white harness, as long as the other white accessories were there....