Kinda feels like the existing suggestions threads ought to be bulldozered in favor of a C# suggestions thread. A lot of the early posts in this arn't taking into account C# changes... and God help the previous thread's suggestions, even though its still stickied xD
Cargo Handling Systems Rework:
I've long felt Cargo Handling Systems are a bit of a sideshow. Most extrasolar colonies are far enough away that even maximum cargo handling times of 10 days make only a small difference. For intrasolar traffic, even 1-2 of these relatively cheap systems is sufficient. CHS do matter for transferring troops between troop bays and dropships - but cryo drop bays have rendered that awkward procedure somewhat antiquated. Additionally, Spaceports are increasing in importance with the changes to refueling in C#, and are more likely to be present. Mostly I use CHS to round out tonnages to aesthetically pleasing numbers.
My suggestion is to drastically increase the size and cost of CHS and drastically increase the penalties of not having them. A sample number would be Size 100 CHS and 100 day standard unload time. (For context, the existing CHS is size 2, a Standard Cargo Hold is size 500, and the standard unload time is ~10 days. I'm unsure of the formula, but a ship with a 1:1 cargo to CHS ratio has 80% less unload time and 2:1 gives it 90% less. ) A ship with CHS would be considerably bulkier and less fuel efficient than those without, but conversely the equipment is much more necessary for rough colonies.
Thus, there are incentives for larger variety in commercial ship design. Bulk transportation between colonies with 1 spaceport can be best accomplished by 1-standard-cargo-hold ships without CHS - they would be the most space and fuel efficient by far. Larger CHS-less freighters would require additional spaceports to load and unload with the same efficiency. Rough-country transports with 1 or more CHS would be much more efficient transporting to unimproved colonies, or to colonies with less spaceports for shorter trips. Colony ships would be pressured by the same design constraints. I can also see a potential role for a "Pioneer transport" - a combination colony/cargo ship that mounts 1-2 CHS specifically for opening new worlds in a specially-designed package, while follow-on traffic is handled by high efficiency ships once a spaceport is built.
As for troops, I would suggest deprecating CHS for troop loading to combat pods from starships. There's already a pretty huge logistics overhead in shipping both dropships and troops to an invasion mission, and combat cryo does exist. CHS could still accelerate the initial loading of troops to transports or to combat cryo. And of course non-combat unloading could still use it. You couldn't really 'get around it' with combat drop vessels since those would cost a bundle more than just slapping on a CHS.