Are you sure about that? From my experience (Blackbeard difficulty) their equipment gradually got better. Speaking of major factions of course, civs and common mutants kept their faith in good ol' powder pistols. Academy, Megapol, Guild, Marsec, etc. all went through their powder > laser > gauss > plasma progression (not every enemy unit on the map but enough). Maybe it's tied to type of ship/mission or them !mission! types one researches, not sure, but it does happen. Feels like intentional progression mechanic to me, and a very fair one at that (except that one early-game enemy hideout incident in July I'm still trying to erase from memory).