Hmmm… I just want to comment on the trains. I like that idea alot. Or perhaps a “highway” of sorts. Something similar to Cowboy Bebop’s space highway. Its like a space tunnel and those inside it get taken to the other side of the tunnel, but if you try to leave the tunnel early, you fall out of the warp and end up who-knows-where.
It would be cool if the tunnel can be a sort of “mini-game” in itself where you can fly your ship/freighter to some defined place and actually maneuver it while the end destination is loading. Maybe if you try to leave the tunnel too early while still in warp, you end up who-knows-where tossed about through space with parts of your ship destroyed from the sudden stop in momentum.
Now, what to do with them?
Players can create them themselves(like Sean Murray said “colonizing”). These tunnels can link to valuable trade routes players have found on their own and others can take these highways too if they choose. These highways can come with a player-defined price to use it, again, if they want to set a cost. Like a ticket or a pass. After all, others will be able to get resources faster this way, people would be paying for convenience and it would add to creating a space economy.
Just an idea with not much thought into it.