I've not found Hunters too much of an issue, Stalkers though are a pain. I generally take up the role of pest control with the Stalwart and let the rest of my team concentrate on heavy weapons to take out the heavy stuff - personally I think using orbitals, etc. for taking out multiple small targets a waste.
I'm not 100% on the armour penetration mechanics but apparently there is some angle aspects to it as well - which seems to be why I was struggling with damage on the Charger's head as where I was thinking I'd have to aim for results in a hit angle which is suboptimal apparently... (not sure if a bug or intended mechanic).