There are so many points on this thread I think are good ideas.
The original post is thought provoking, and may even have been a better model if adopted from the outset.
Unfortunately (or not) we are where we are. Working out the consequences of such a change makes it very difficult to see how discovery would be recognisable.
One thing you could edge towards is a system where freighters are still cheap... and they do enough to generate the funds for fighters, however the transports and trains are all very expensive and only factions can club together to get one... rather like they do now with battleships. Indeed if you did this cap-ships would only be available to those factions who had enough economic muscle to get a trader and then run it and keep running it.
Additionally if you made the trains expensive to restock after death it would mean the faction had to hire people to keep them from dying. Also it would mean that current freelancers who had them would actually not be able to make a profit keeping them on the road wiothout hiring lots of help.
Obviously they would need to bring in big credits for these to sustain all of this effort.
As for the dynamic trade system, I believe it has been mentioned several times and Igiss has ruled against it as too much effort. I know there was a mod out there that did it automatically but I really don't know whether it worked or used up too much server resource.