I am tempted to have something like civilian shipyards, or 'build capacity', or some other 'on-map' capability, but it might turn out to be a lot of work without any major gameplay impact.

If Raiders and NPRs attach and destroy these SYs, these infrastructures do have big impact on a player development/expansion, IMO.
A player could give money, upon request or voluntarily, to commercial lines to help them and rebuid their own yards and ports. Or commercial lines could lend a player (even NPR) civilian yards to rebuild their fleets, until their own infrastructures are out of work.
Maybe software implementation of this can be tricky, but I think gameplay could gain some interesting twist.

About your 5 points:
1. Agree; but you can also consider a fee for moved tonnage/people and/or for moved volume: 1 kilogram is much less than 100 kilograms, and requires less fuel to move it, but 1 kilogram of feathers, straw or cotton wool can be more voluminous than 100 kilos of metal, so requiring a larger ship (in principle)
2. I think of different incremental building costs for the different ship types: e.g. (purely cosmetic, to illustrate the concept!) colony/passengers at N^(3/2) (thanks Nuclear!), freighter/cargo at N*log(N), defence/security/armed ships at N^2 or more, costs that increase even more with the ship tonnage. About these defence ships, I can think about a security branch of a company, with its own defence infrastructures and ships to protect line sites, acting like a sort of a minor NPR
3. Together with the number of ships, also travelled distance can be included (from the start of the shipping line or in the last X months)
4. OK
5. OK (to keep its management simple)

Thank you Steve for your dedication!

Quote from: Steve Walmsley on Today at 11:59:18 AM

5) Have a simple retirement limit, such as 20 years, so that new ships are cycled in.

Should probably tie this to racial research modifier, or possibly even tech level. So that lines aren't being overly "wasteful" by scrapping and replacing ships with (near) identical copies if the player hasn't made any significant tech progression. 20 Years would probably be a good baseline but if you are playing with limited administration and a 20% research rate, a ship would have a much longer useful service life and could hang around for another couple decades before reaching true obsolescence

I would be very hesitant about any hard cap on years in service from a roleplay perspective, admittedly it is a minor point but in a WH40K setting for example where ships serve for hundreds or thousands of years, it would be odd to have a 20-year limit for civilian ships. Again, very minor and probably not very noticeable but all the same.

Tying the length of time to game settings, tech level, etc. is at least a better solution, therefore. I don't think such a limit is needed in practice, though, if the civilians have an effective cap on ship numbers due to "maintenance" fees then it hardly matters if they scrap ships or keep using the ones they have. Once tech advances then they can scrap the older ships for newer, better models of course, as they do now.

The other ideas in Steve's reply seem good to me.

1) Payment based on distance in km, not transits

If you go through with this change, make sure that you make it so that transports will be weighted towards picking routes that make them a decent amount of income, instead of doing Earth <-> Moon runs for pennies on the dollar.

Being honest, I like the way the civilian lines work now and like the experience you are describing Steve because it makes the growth of the empire feel organic to me.

That said, could we add some kind of mechanic where if a civilian ship sits idle for too long the line decommissions the ship? In game it can be explained as a company doesn't want to pay for maintenance of a ship that isn't doing anything. So if you want to decrease the number of ships you just mark a bunch of colonies as stable and wait for the ships to disappear.

I was about to suggest exactly this one.

To implement an "autorefresh" function for open/background windows.  You can use browser extensions like "Auto Refresh Plus" for Chrome or "Tab Auto Refresh" for Firefox. 

Are you saying that these browser extensions can be used to refresh non-browser windows?