The AMR SHOULDN'T be a big gun. Yes, it is big, but size/weight isn't what makes a big gun - as EnderDragonFire says, it's the grip. "Small" guns aren't limited to SMALL guns - it goes right up to the sniper rifle in FO3, so I don't see why a slightly larger .50 cal rifle would be any different.
If it's grip only then the LMG, Bozar, Automatic rifle, and 25mm Grenade APW shouldn't be Big Guns either since they all share the same grip in the GECK with things like the AMR and Assault Carbine. I don't think anyone would argue with the Grenade Rifle being included as a Big Gun.
I think the basis of Roy's list was weapons that met more than one criteria. They were weapons that were classified as TwoHandHandle, TwoHandLauncher, or they were TwoHandAutomatic style weapons that had ammunition that was already considered explosive (the grenade rifle,) or were high strength/high weight weapons that were awkward to use regardless of grip style (the AMR, Bozar, LMG, and Automatic Rifle.)
The Gauss doesn't fit in with any of those criteria. Probably why he left it out in the first place. The only reason I could see it being included was for balance reasons. If the high damage scoped rifle was taken out of small guns then the high damage scoped rifle should be removed from energy weapons too. The high damage output of the Gauss is the only thing that could logically qualify it as a Big Gun as it isn't heavy, it isn't large, and it doesn't use an ammo type like missiles or grenades that would make it an obvious inclusion.
I'm just playing devil's advocate here, I don't care which way these weapons go in terms of skill requirements. I just like to try and get all possible views out there for the developers to consider. I suspect Roy has already considered a lot of this when he made his original list though.