I agree that the Attractiveness point value, at least, seems a little disproportionate, but I think I followed the core book's Attractiveness entry precisely. At -5, "people will be taken aback", and both super mutants and ghouls are ugly enough to outright cause revulsion and fear. "Beings with inhuman features can have levels as low as -10." -6 seemed appropriate - both ghouls and super mutants are always more hideously ugly than any human (human-looking human, anyway).

I'm pretty sure that Attractiveness is intended to be either objective or measured against humans, and it definitely makes sense to me that super mutants and ghouls would get penalties to interacting with humans.

There are two problems that come up:
1. Ghouls get an intimidation bonus? On first blush, this seems inappropriate - but I'd say that's just because we rarely if ever see or hear ghouls trying to be intimidating. So it's just that they never try to intimidate, rather than that they are incapable of it. And the feral ghouls in FO3 are definitely scary and terrifying (even to me as a player!), if not quite Fear Test material (unless they jump you or you've never seen one before).
2. Do ghouls and super mutants have penalties and bonuses to interacting with each other, based on Attractiveness? This one's easily resolved: no. They ignore Attractiveness among themselves (or altogether, maybe; why would a super mutant care if that human is pretty?). This seems like a good general rule: Quasimodo (Attractiveness -5) won't care about Caliban's deformities (Attractiveness -4), because Caliban is comparatively more handsome.

I think I will definitely use the drawback you came up with. I might make it a 2-point one with a -2 penalty, because I think I'd like to make it significant. Super mutants should have a hard time using the tools and small arms of humans.

Where's Natural Toughness from?