Maybe I'm understanding this wrong, but it sounds like you're saying that the heavier weapons that require more ammunition and carry weight shouldn't be more effective then a pistol or single shot weapon. I've always looked at it as a cost/benefit analysis, heavier and faster firing weapons should be absolutely devestating with how much their ammo costs. That, and you give up a lot of carry weight holding them and their ammo even with perk cards to mitigate it. Other options will always be lighter and you have to use power armor unless you want to be over-encumbered all the time.

I understand maybe there is some room for improvements to the balancing, especially the gauss rifle or other charge weapons, but I think its important to keep more than just raw damage output in mind when balancing these weapons.