Right now when two fleets meet, it's a flurry of bullets with everything shooting randomly at everything else (as far as I can tell). This may already be planned, but it would a wonderful feature to have engagement protocols. For each design, just a basic setting to give it some idea what kind of ship it's designed to shoot at. For example, you would have ships that were designed to shoot at ships smaller than themselves, mounting torpedo launchers and lasers. Whereas you have other ships that are more purpose designed to shoot at larger ships, mounting missile launchers and hyper-dense lasers.
This design methodology is already present, it would be nice to have a setting that tells your ships to take advantage of it. Perhaps this already planned? Or . . . shocking as it might be, might your ships already do that on a weapon-based level? I haven't noticed any bias, but I could just be missing it.