Honestly it'd be cool if you could essentially customise existing hulls beyond weapons/hullmods/flux. In other words, the ship design inherits the basics of sprite, hitbox, weapon mounts, engine placements - and from there the player has points to assign to flux stats, weapon mount types, ship system, built-in hullmods, engine speed, armour, maneuverability etc.
It would bascially be in-game modding, and would require a lot of retroactive assignment of those points and determination of those base stats so it'd definitely be impractical, there's no argument about that. It'd also probably result in some pretty OP builds but I digress.