there is no easy answer to the capwhore problem. i'm afraid that anything we do won't do anything to remedy it.
at the moment capships are fairly weak, the mod has been made so that fighter class ships can more easily take down big ships. there always has to be balance so that things don't get out of hand. aside from just a few known balance issues i.e. gunships/gunboat & cruisers being either slightly too powerful or slightly underpowered, everything is fairly balanced.
all that being said i think Igiss has down a great job of balancing things so that in the end, it comes down to player skill. no matter what you fly, if your good enough you can just about take out anything in anything.