The missile cruisers can shred capital ships to pieces with their missiles. I think that is what they were designed for. To make up for their extra cost, either change their missile pods to the top and bottom and make them turrets, or add a top and bottom missile turret, and have them circle their target at range unleashing their carnage!
would that not made them somethink similar to destroyers? I think that Javelins are created based on old good torpedo boats, or torpedo centrewd destroyers. It would make more sense to create a new unit that would fill the gap, somethink more expensive armed with more powerfull missiles, or more misile lounchers, and add some autocannons, like a WW2 torpedo focused destroyer or Light Cruiser and decresing the costs of missile cruisers. I would put something like this between Cruisers and Capital Ships. In wider perspective, i thiuk that expanding the lineup and adding new class, like destroyers, that would have the firepower to fight a Capital Ship, like some... 6 or 7 against 1, but with armor of a Cruiser class would add refreshing toutch, while changing the balance. Like what if every race will have a specialized Destroyer that would differ in stats depending on Race and Loyalist/Separatist choices. (ybh this game needs somethin more than hd refubrish and orbitting planets. more tech, more ships, more independent factions, new playable faction? i just hope) And yes, I know it takes lots of work.
all best and ceep worm