So many ships are handicapped only for the bigger ships to give you an illusion of progress.
Mainly module size and unique outfitting slots, like the military compartments we already have, should differ between ships.
I'm not saying my Diamondback should be able to haul a 100t. I'm saying restricting how many features a ship can have is not fun. There is a reason small ships are not used a lot in this game.
Here are a few improvements i can think of:
1) Multipurpose scanner and multipurpose limpet controllers
2) Much more size one optional and utility slots
3) Planetary vehicle (and or others) as standard modules that come with every ship like the planetary landing suite
Engineering already ensures that every ship can become truly unique in it's own way. So I don't think this would reduce diversity of builds.
I just don't want to choose between a manifest or kill warrant scanner. Seems stupid. Nor do I want to choose between a reckon or a hatchbreaker limpet controller. Etc. It's bad game design that's based on restrictions rather than rewards.