OK, I've read back though and we are getting quite complex
I still like some of the proposed changes though so lets go back to a simpler version.
This all began because I was answering a question on replenishment at the same time as other orders and then suggested moving all logistics into orbit. The subsequent discussion went from that point because we needed a reason to keep ships in space. That reason then sparked a series of different consequences. So how about this instead:
1) We have technobabble that states ships can't land on planets, so logistics is generally in orbit (fuelling, cargo transfer, maintenance modules, etc). This will make non-planet based logistics much easier and will makes orbital space and the early game more interesting
2) if a planet exists, the logistics facilities will draw on its resources, otherwise they will use their own.
3) If orbital facilities don't exist, ships can mount 'shuttle bays' that allow slower interaction with the planet.
4) If ships can't land on planets then, under the current technobabble, there are lots of potential consequences around fighters and missiles not being able to move from surface to orbit (and vice versa), with subsequent impact on PDC hangars, ground-based weapons, etc.. Instead, we could change the currently proposed technobabble by saying that turbulence in the fluidic Aether near gravity wells is proportional to the mass of the object moving through the Aether. Once that mass exceeds 500 tons, there is a serious chance of damage to a vessel.
Now we actually have a reason for the previously arbitrary limit of 500 tons on fighters and all the complexities around fighters and missiles go away. It becomes very similar to the current game, except that we have logistics in orbit. How does that sound?