While user made missions would be great, unless you plan to have the system be very complex with control over broad aspects of the game, it likely won't see tons of traction and thus be less important.
Basically, either go all in on user mission customisation and feature modability, or save such things for later.
That is my take at least.
The plan with user-made missions is just to give you the tools that I used to create the story missions myself. You'd be able to do everything short of locking locations or actions (as those things are permanently written to your save file.)
It's purpose is just to give you something more to do once you complete whatever amount of story I have in the game up until that point.