You probably upped mitigation in the per level upgrade or something.
As far as resiliency goes, you can do a lot by making the max mitigation high for capital ships, then go into the race files to lower the increase rates. By using their typical dps against themselves as a benchmark, you can curve damage to become near flat with increasing firepower. Set the return rate to whatever you want to be optimal damage, and then set the increase to add percent mitigation changes with regards to your damage value.
I've contemplated doing a rebuild centered around it, but I'm just too lazy. The way they handled the mitigation values in Sins depressed the hell out of me after putting such a system in there to begin with. It can be used to force decentralization of firepower by penalizing group target selection.
