I think the trick is, the smaller ships weren't -meant- to be used against the bigger ships, at least not at the MM end.
I'm working on a few ideas for my mod, intended to expand -both- ends of the spectrum ... bigger ships, and more viability for swarms of smaller ships.
For one brief example: a new Racial Trait, giving a racial technology: "Microscalar Construction" is the current working name; the theme is packing more function in, per kT, than anyone else ... and specialising in very small hulls, comparatively speaking. Eventually, I hope for a Microscalar ship to be about as good, in total, as a ship twice it's size (and probably only moderately less expensive than such a ship, as well). Possibly,much of it will be an ussue of Mounts for Microscalar races, if possible to work only on ships at or UNDER certain displacement levels.
Also, hull modifiers (if it's doable) will reflect both to-hit AND to-not-BE-hit modifiers; smallers hips will not only be harder to hit, they will be more able to SCORE hits ... owing to relative maneuverability.