If there are plans in the future to revisit the civilian shipping, my suggestion would be to go the route of 'established trade lanes'.
I.e. A civilian shipping company will only build up to X number of 'free roaming' traders which simply look to whatever supply and demand are available.
The rest of the shipping company's ships instead take on established routes and then just repeatedly run that route.
Refer to the image for more details, or the text from the help button mockup below.
Text in help button popup:
This lists all established trade routes.
The assigned fleet (if any) continually moves between source and destination. The fleet will always attempt to fill its cargo. If possible, it will also attempt to move goods from destination to source during a return trip, if supply and demand permits.
You can subsidise trade routes (even ones that do not yet exist).
When subsidized, the assigned company will assign additional ships (and always at least 1) to the route. The company will take 1 wealth per 10 000t of goods moved per 30 days, and also 10 wealth per 10 000t of empty cargo space (if supply or demand does not allow a full haul).
This subsidy cost only applies to trips from source to destination, return trips are not costed.
Note that the subsidy is paid on loading the fleet at the source, failure to pay the subsidy in full will result in a ship being unassigned from the trade fleet. If this was the last ship on that trade route, it will not do the run, and the last portion of the subsidy is lost.
If a subsidy runs out, normal considerations of the viability of the trade route apply. Unviable trade routes will be removed.
A trade route is viable if enough demand and enough supply exists to fully fill at least 1 ship, and a round trip does not take too long to complete.
Whenever a fleet on a trade route fails to find enough goods / colonists to fully load all ships, the fleet will immediatly unassign one ship from the fleet (it becomes a free roam trader) and attempt again. Repeating if needed.
If a fleet is emptied completely (i. e. cannot sustain even one ship) in this fashion, the route is deleted entirely (unless a subsidy is in place, in which case at least 1 ship will remain assigned as long as sufficient subsidy remains).
Every 30 days, if a viable trade route is being under served, then additional ships will be assigned to the fleet.
For free roaming traders to be assigned to a trade fleet, they must at least be within the same system as the trade route.
If a large demand and supply potential is unmet on a trade route, a ship might be specifically built to be immediately assigned to that route.
If a subsidy exists on the route, and the subsidy is large enough to cover the costs of a new ship, a new ship will be immediately built for that route, but funded directly from the subsidy.
Verbose button changes the table / column layout to full sentences.
A trade route is automatically established (without any need for subsidy) under the following conditions:
[list]
[li]A destination with demand exists.[/li]
[li]A source with supply exists.[/li]
[li]If the travel time (distance / speed of relevant 'newest' design) between source and destination is TT. And round trips per month is (30 / [2 * TT]) = TPM. TPM must be greater than 0.5 (At least 1 trip in two months)[/li]
[li]For trade goods, the demand must be greater than 1 * TPM * 'Newest design cargo space' / 'Size of trade good'. I.e. the ship must be able to make at least 1 full cargo haul per two months.[/li]
[li]For colonists, the demand must be greater than 20 * TPM * 'Newest design colonist space'. I.e. the ship must have enough foreseeable work for at least 10 months.[/li]
[li]For installations, the demand must be greater than 20 * TPM * 'Newest design cargo space' / 'Size of installation'. I.e. the ship must have enough foreseeable work for at least 10 months.[/li]
[li]The source must be able to meet this demand.[/li]
[/list]