I felt that was one of the more significant issues I'm having with champions right now on my first whole playthrough; ideally I want champions to not simply be just another ship, which sadly wasn't the case in my experience. I played a glass cannon spire ship outfitted with beams and one forcefield module for nebula missions specifically to wait until it gathered enough energy for 4-6 forcefields before soloing a starbase with my hands on ctrl+q... it was effective and all I did, but consequently it didn't feel visceral or engaging. As a ship in the fleet, it was basically another starship that was really disposable; I feel champions really need to be distinguished from an FRD-able ship with modules, but of course striking the balance of being not too overpowering or overly-demanding of micro.
And curious, but are the [possible] upcoming missions going to be all "defend the base" situations?