1) Adding additional die for energy weapons might not be the route to go.. maybe adding stuff like conditions/modifiers.. get hit by a laser, quick burn.. get hit by a plasma weapon, going to burn more, or not a nice clean burn, make them save Fort vs pain of the hit, and pain causes penalties to attack, skills. Or can have plasma weapons have knock down feature (as plasma generally has more mass and kinetic energy over photons of a laser), then the target has to spend time getting back up if they are knocked down.
2) not sure what all modifications Fallout games have..
3a) colourization.. generally not really.. would be neat signature for specific weapons, or a way of identifying friendly/enemy fire in the dark if everyone on the same team uses lasers tuned to a specific colour. HOWEVER.. certain frequencies do affect colour.. laser firing in IR would be more.. red? And UV frequencies more purple. I have Green-Blue lasers which are a green-blue colour and operate underwater better than regular lasers, so that's where colour could be a factor.
3b) For my upscaling.. I have rules for upscaling weapons, or crew served/vehicle weapons, some are just increasing damage by a die or two, or adding ignoring dr/hardness. Check my thread for it as I can't remember what page it's on off hand.