The is the one big combat thing that, in my opinion, needs to go away completely.
There is no reason for this penalty to exist and all it does is drive a linear progression in a place that a person simply doesn't need it.
Weapon damage growing by weapon size is all that is needed to delineate the hardpoint sizes, this penalty is an unnecessary addition that does nothing but outclass smaller ships before their time comes up.
In my opinion, the best examples of this are the three earliest fighter ships and the Asp.
The eagle is a fun, fragile little ship with three well placed hardpoints, but it obsoletes itself for "real" play very quickly solely based on this penalty. Without the penalty, this could be a ship preferred by those who really want the fast and nimble feel of this little fighter, and could make up for its lesser damage(3 small hardpoints) by using the ships other strengths to avoid being hit.
The Viper/Vulture would suddenly become a bit of a debate, as the Viper would come with the potential flexibility of having four hardpoints and greater speed, whereas the Vulture would have the advantage in raw firepower and its notable lack of flexibility in armament would suddenly become an actual issue worth considering. The way it is right now, the Vulture is a no brainer if you want to even consider making timely work of any large craft for bounty hunting based almost exclusively on this penalty(you can avoid most damage with either craft by piloting to the areas weapons cannot hit you).
The Asp would hardly be overpowered, but its six guns would be quite formidable without this penalty and would be as favored in its "weight class" as the cobra is in the small class if this where the case(it's still heavily favored for its other qualities, referring to combat here). By the time you're fitting and flying an Asp, being able to take down big game is a real consideration and as is, four of those guns are borderline useless against any craft larger than itself.
Removing this penalty would breed diversity that's good for the game at large, and really it'd be good for the bottom line dollars, too. For example, the Viper has more paint schemes available for it than any other model out there, and really I'd love to snag a few. I won't though, because I'd have to take a purposeful step backward in overall ship quality in order to actually use those skins. Unless a person chooses to accept a far slower rate of income and a more or less self imposed hard limit on the content they can handle, progression it an outright necessity and in my opinion this detracts from the game.