DAMN!!! That is a really solid setup for a serious game. Two things that are worth thinking through, in my opinion, are transfer ports-stations that the player can place that allow docking ships to leave cargo for a ship from another line to pick up and giving the player more control when routing waterways. I had a situation where a black port spawned in a place where it was literally impossible to attach it to anything.
I'm currently trying to make a game similar to Mini Metro, but with interplanetary transport, and I have to say, this project gave me quite a few ideas for my own.