are the capital ships supposed to be as squishy as they are?
On the contrary, most are extremely tanky, with UNSC capitals reaching 12-20k health by the end-game, vastly outstripping the more common warships. What you're experiencing is a mix of the hard-and-fast pace of the mod, as well as a product of the AI's prioritization of capital ships and titans as targets, often focusing them down in place of the standard frigates and cruisers. Even Infinity will be brought down in moments by an entire fleet.