General gameplay trope - the guys with ranged weapons and more casualty-averse tactics tend to be the good guys, and vice verso for the bad guys. As for fighters, it's sort of codified by star wars: if a space battle consists of a bunch of fighters and carriers on one side, and a bunch of large warships on the other, then the first group will usually be the side the heroes are on.
As Nettle so succinctly pointed out, fighters result in pretty high casualties! I might agree they are "good guy" fodder in movies and the like because a fighter is naturally going to be the underdog in any ship vs ship battle, and also because a fighter is an individually piloted ship that allows a character's skill to be shown off without being diluted by the capabilities of other crew members, but I really don't see that applying in any way to Starsector. The way Starsector is completely disconnected from in-game casualties (going as far as their being a basic commodity to buy, sell, launch out the airlock, etc) coupled with ships often being hundred or thousand crew affairs, lends the setting more of a "life is cheap and the price is often paid" air than that of a "scrappy underdogs fight against the evil empire while lamenting every loss" air.
To put a more cynical spin on it, beyond the standard "oligarchy dressed up as freedom fighters down to the standard set of design tropes", you could say that an organization made up of multiple polities has an inherent desire to make sure that nobody's death can be made out to be the fault of someone else - especially someone from another polity, who might be commanding a multi-national fleet. DEM torpedos so that nobody in parliament can say that the ship crewed by their people was arbitrarily chosen for a close-in bombing run, fighters so that the majority of losses can be attributed to pilot error rather than the mistake of a captain with a distinct homeworld and set of political benefactors, and fast midline ships so that the disparate set of officers can make full use of initiative without needing perfect coordination, rather than relying on more rigid, error-intolerant phalanx tactics befitting a homogenizing empire like Rome (or the Hegemony).
Essentially a gentler version of the SD getting penalties because of their system of government - political concerns determine force composition and strategy, not necessarily for better or worse, but certainly in directions orthogonal to building a strictly optimal fleet.
On the note of life being cheap but still needing relatively wise spending, does anyone else have an opinion on giving the SO eradicator a shield so that it isn't as much of a free kill in mid-late game?
