Combined with the basic overhead of designing a spaceworthy ship of any size, small ships simply aren't cost-effective if you can build big. The main remaining use of a fighter as a scout ship for long-range patrols is sometimes seen, but even then ships have long-range sensors allowing a skilled operator to ascertain the approximate size and nature of an incoming force much faster than a patrol ship could be sent. Downscaling most of these weapons would reduce their effectiveness, which would already be minor against a heavily-shielded capital ship. Systems like phasers and torpedoes are both so powerful and easily-aimed as to destroy many small craft with a single shot, and so bulky the system wouldn't fit in most small craft. The Gene Roddenberry universe is dominated by weapons, sensors and defensive systems that would generally render 'fighters' as we know them useless in battle.
