What if we kept the same armor system, and only gave armor (in significant amounts) to only a few ships that use it as a distinguishing trait? So basically, tanks and armor ships and stuff. The thing is, if that was the case we would still have the problem of low damage high rof ships being bad against armor... but those aren't the ships that are supposed to fight armored ships. You bring in different ships for that. I'd even go as far as to say stuff like golems don't even get armor, unless it's explicitly supposed to be heavily armored (the armored golem). So, basically, either armor exists as a significant distinguishing ability, or it just doesn't exist on a given unit. We'll have the triangle ship that's kind of meant to armor pierce like you guys are saying... and that honestly seems like a decent way to go. So, you could end up with something like this.
Frigate: Slow, long range, lays down anti-armor fire from a distance.
Fighter: Expendable ships, armor plated for extra armor and health while they intercept bombers and take hits for the expensive ships.
Bomber: Very slow, vulnerable, but able to take down any heavy defense in the blink of an eye.
Well... something like this. Basically, whatever kind of triangle role discussion you guys are all talking about.