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Does X4 Foundations count? I mean, in the broadest sense transport is an integral part of it, right? Flying and defending valuable cargo transports yourself, or establishing automated trading routes with a fleet of NPC ships, or mining resources and building space stations to resell or refine them, or ambush other ships and take them over or blow them up and scavenge the wrecks, the universe is your oyster.
Granted I'm a noob and have rather little to show for myself considering how many hours I've already sunk into it. The game explains relatively little, the menus are pretty unintuitive, I haven't played the series previously, so the learning curve is rather cliff-like. However I have a pretty nicely outfitted player ship (pic unrelated because I can't seem to take screenshots myself) and some savings now, I've tried out all sorts of things to get an impression of what I can do in the game, and most recently I've found half a dozen abandoned medium sized transport ships in mine fields in various places in the galaxy. They're now all in docks awaiting some equipment changes and then I'll see whether I can set up some automated mining and trading and maybe finally build my first station.