First of all, I love your suggestions.
My only issue with varied system sizes is that the system slices on the power wheel are already as small as I could make them (considering that they have to be easy to read on small screens) and if I make them bigger it'll be difficult to fit all of the required systems on the wheel, and allow for enough variety between ships or ship variants.
Each system on the wheel is a slot currently, which you install equipment into. Each slot has an equipment type (turret, shield etc.) and a class from 1 to 5 (1 being the weakest and 5 being the strongest). A class 3 turret system slot could take any class 3 (or lower) turret for example.
We do have different power wheel configurations for each ship, with different system types and in different places, but these are in the form of variants. Variants will allow you to choose a ship to suit your play-style. I don't think we can allow power wheel configurations to be customised beyond that because it would lead the min maxing of ships, where the community figure out overpowered configurations and everyone uses those.
