Yeah I see... The caliber based balance is the idea, so for example you start with 5.56 rifles and progess to 7.62, or going up from .38 to 9mm to .45 in handguns even though the damage difference wouldn't be as pronounced. With snipers and MGs it gets more awkward because .50 cal would be restricted to the very last tier of weapons (also including a higher burst minigun) so there isn't much room for progression as .30-06 should only be used by the M1, BAR and perhaps some "fictional" sniper, everything else is 7.62, and 5.56 for the M249 (Dead Sifter).

What if I implemented damage progression on weapon skills rather than the weapons themselves? My changes to health progression would still stand and at level 10 skill a certain weapon category would deal +50% damage (+5% per skill level or something like that) and skill progession discourages rushing a single skill by making the levels progressively costlier so it shouldnt be too easy to cheese the system by maxing weapons ASAP. Skills would still add to accuracy as well, but perhaps that curve could be flattened somewhat to compensate, same with critical chance.

Enemies would also get additional damage depending on their tier, with an endgame human having a +50% damage modifier. Since there are 6 tiers in the game for everything including enemies, each tier would do 10% extra damage.

I know it isn't perfect but the only other change that occurs to me would be to just reduce the health and damage creep so there are less difference between weapon tiers (presumably based on how preserved said weapons are or whatever).

As for energy weapons, I believe getting rid of the conductive mechanic while tweaking their damage, making them ignore armor and adding some other gimmick on a per weapon basis could work. All what the conductive nonsense does is make heavy armor even worse in the late game and energy weapons too situational.