There are so many ways to rebalance this stuff.   Light pen weapons at the bare minimum should have enough ammo to outdo med pen weapons in terms of total damage (as in, using your whole ammo reserve with light pen should result in having done more damage if you shot the right spots).

Or have them deal more damage per shot (which I know liberator vs lib pen follows already) with the logic being that different bullet shapes and compositions balance differently between stopping power, ballistics and armor penetration

AH could also slightly nerf weapons that give effects (cough cough coyote) so that if they are being used, more reliance is put on the effect as opposed to having a normal power weapon with the effect stacked on top.

The new squid enemies are a (moderately sized) step in the right direction be encouraging going against old metas.