How about a new ship design anti missle frigate or give the flak ships an ablity to chose anti fighter or anti missle focus{ie they can only defend against 1 type of hostile and while anti missle they cannot shoot other ships} Anti missle effect could target any kind of missles they larger missles would take a few hits to knock out Some upgrades to these ships could include damage/faster rate of fire and range you could have missle upgrades too phased missles {
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