The reasons fighters dominate Sci-Fi movies are:
1) Adventure-type movies need individual heros whose actions make a big difference. A lone fighter jock (Luke Skywalker) or two (Starbuck & Apollo) taking out the big bad guy threat to the galaxy fits the ticket. Bill the Galactic Hero and the Reverend First Class Fusetender Temba down in the bowels of a spacegoing battlewagon, replacing fuses in the shield system as the blow under enemy fire, does not. Star Trek works the way it does because Roddenberry's original concept was "Horatio Hornblower in space" - the model was naval combat in the age of sail, when by & large bigger was better. Small ships were more maneuverable, but their broadsides lacked both range & power to be a serious threat to a ship of the line. That is what "ship of the line" meant - a ship that was big enough to serve in the line of battle in a fleet engagement. The small stuff was used for scouting, patrolling remote secondary theaters, chasing pirates (who couldn't get their hands on a ship of the line), raiding enemy commerce and escorting your own merchants against enemy commerce raiders. That is mostly because ships of the line cost too much to use for every mission. This was pretty much how naval warfare worked from the advent of guns until the invention of the self-propelled torpedo (which made small nimble ships a threat to capital ships). However, in that kind of setting your heroes end up being establishment-type senior career officers, rather than farm boys in whom the force is strong or rogues who gamble & wench in between Cylon attacks
2) In the most recent large-scale naval war in history, carrier aircraft dominated and battlewagons were reduced to a secondary role. That is what is most fresh in the public's mind - that carriers have made battleships obsolete. Make different assumptions about the effectiveness of anti-aircraft defenses and this could change. For example, in the "Hammer's Slammers" stories tactical aircraft are hopeless. If armor/shielding makes battlewagons relatively invulnerable to any weapon small enough to mount on an aircraft, and automated high tech air defenses swat planes out of the sky before they can do any harm, suddenly the battlewagons make a comeback (if you also find a solution to the submarine threat, that is).
3) Moviemakers copy a successful film. Lucas is reputedly fascinated by WWII air combat, and Star Wars shows it (the Tie Fighter vs the Millenium Falcon sceen could have been ME109's vs a B-17, the Deathstar attack could have been any of the Pacific carrier battles). Star Wars made bigger $$$ than any movie up to that time. So, everybody else copied, except the Star Trek universe which already was locked into a different model.
In the end, it is a matter of how the designers want it to work, since there is no "reality" to model. I personally like a game where the battle line is at least a viable option. I'm OK with all carriers & fighters also being viable. I think having fighters sitting out in space forever "feels wrong", but I do it myself since it is advantageous
If I were the designer, I'd let fighters fly off on the system map the turn they take off but make them land by the end of the turn or be lost (like in Civilization).