I'd like to throw my hat in the ring on this one.
I could envision two separate types of civilian shipping operations. One would be short-distance (3-4 jumps) general trading, which we have now. Specify supply and demand amounts as happens now. To combat civilian fringe-lock (where freighters get stuck on the fringe with no contracts to lure them home), have each shipping line have a home system. Instead of using the current location of the ship as its source for searching for short-range opportunities, it uses the home system. Idle ships gravitate back toward their home systems. This would set up regional "hubs" of localized shipping. A disadvantage to having this system in place is that freighters will spend a larger proportion of their time empty as compared to now. I'd compensate for this by reducing operating cost and increasing the income ships get when they DO perform a delivery.
To move that mass driver 4+ jumps across your empire, you'd utilize a new addition: long-distance (LD) shipping. It would require a special UI, but the way it'd work is you'd specify your origination point and the destination point, as well as the specific cargo. I. e. , instead of having 200 mines "up for grabs" on Earth, and 40 mines "generally wanted" at Omicron Persei 8, 7 jumps away, you'd specify, "Deliver 200 mines from Earth to Omicron Persei 8". As soon as you "confirm" this contract, the game would calculate the route and a general profit/time rating. From here there are two options:
1) A local shipping company as above would decide to take this contract and allocate enough of its freighters to execute it.
2) There are specific shipping lines who only deal in long-distance contracts.
In the long run, I'd like to see companies make bids on long-distance contracts. So you'd make the contract public, as it were, wait some time, and each line would evaluate its ability to execute the contract, its estimated profitability (based on the number, capacity, and speed of its freighters) and submit a bid, with some randomization in to simulate undercutting and edging profit margins. In the very long run, lines could receive perks for being regularly chosen for LD shipping contracts.
I think this addresses the common concern of having to get components halfway across your empire, while still allowing the more free-form localized trading. There's not a huge performance hit, as the pathfinding for LD contracts is done when you create the contract, instead of at every interval, and the lines only decide whether or not to take the contract one time (or, perhaps, each time they launch a new ship that adjusts their total haulage capabilities, and the contract still exists, ).
If you were really savvy or into micromanagement, you could setup hub+spoke models, where you ship installations directly between two "hub" locations, and then allow the local shipping lines to distribute the installations according the short-distance model. Alternately, it could be that the only viable destinations for LD shipping are locations with commercial spaceports, maybe even to the point where to be eligible to be an originator or destination of a LD contract of X jumps, the location has to have a spaceport of size X-4 (or 3, if you limit local shipping to 3 jumps). I. e. , a 5 jump contract would require a size 1 (or 2) spaceport at each end of the route. This gives spaceports a role besides being cargo handling improvements.
Regarding trade goods, on a local level they'd work the same. On a long distance level, I can envision "trade partners", widely separated colonies that engage in LD contracts with each other behind the scenes, based on their spaceport level.
For refinements, I'd like to see civilian spaceport complexes built up on inhabited colonies rather like civilian mining complexes are now, perhaps based on trade income at that colony, obviously with diminishing returns. Thus, while you could manually expend the resources to build up your trade infrastructure at some world, if it was naturally generating a lot of trade, the civilian sector would build up the world itself. Diminishing returns obviously.
I'd also like to see freighters cost less as time goes by since the design was first produced and/or the number of ships of that class increases (though this is something I'd like to see for all ships, not just civilian ships). One final little niggle is that I'd like it if we could specify that a ship design is a derivative or refit of a different design. I. e. , my Outreach Mk II freighter is a derivative design of my Outreach Mk I. Flagging them this way would allow me to more easily refit my own, and more importantly, allow the civvies to refit their ships if they felt it was economical to do so. Civvies would only consider refitting ships to a new design that was marked as derivative of the current design, and would not step down the chain. I. e. , if I also have an Outreach Mk III, that is a derivative of the Outreach Mk II, a civvie will not consider refitting a Mk I to a Mk III. It will only consider refitting to Mk II. It will also never refit if it is cheaper to just build a new ship to get the same increase in "haulage capability".
So many thoughts!