I have spent some more time looking at the actual game files, and tweaking and testing various entries. A few notes:
1) Assault Fighters (first and last carrier modules) are coded to have (at least) one of every type of weapon and defense. Also, every Race Assault Fighter class definition (as noted earlier) is coded as Tiny.
2) Drone fighters will have lots of beams, some shields, and thrusters. That's all that they are allowed to have.
3) Guardian Fighters get Kinetics, Armor, and maybe shields/point defenses (if they fit).
Seeing this, it really makes me think that the intent was to start out with a general all-around fighter, then you could specialize depending on your own weapon focus (beams or kinetics). I do wonder why there is no bomber-class, which would allow missile heavy players the ability to specialize their fighters too. Too powerful maybe?
I'd really like to hear from the developers if the Small/Tiny issue is intended.
Regardless, I have now modded my own game so that all fighters are tiny, Assaults prefer missiles, and the High Capacity carriers no longer add fighters, they multiply whatever other carrier modules you have (so high capacity works for drones and guardians, not just assaults). So far fighters are still pretty powerful, but not as insane as they were!
Edit: Part of my point that I forgot to make, is that the differences between fighter types are not just hull size; weapon type and defense load-out significantly affects their effectiveness.