First of all - all the changes look great!

At the topic of civilian shipping lines (hope I'm not late to the party), would it be possible to organise the civilian ships into some kind of convoys? Right now every ship is in its own fleet, which leads to tens if not hundreds of civilian fleets flying around.  This would declutter the map while still being able to see the CIVs on screen and could potentially limit the late game lag, since the civilian AI would calculate the decisions for lower number of fleets.

After a boarding action I have the transport shuttles load ground units from the captured ships, I suspect any troopship could load from the stationary ship

We never stop from learning with Aurora, thank you 

Interesting changes! Not sure if I should continue discussing here, or move to the change discussion thread, but since we're here...

Will we still be able to set colonies as source or destination or stable?

Also, would it be possible to set taxation on shipping to be negative i.e. to offer incentives to grow their fleet, particularly early on?

Lastly, the changes don't seem to address the balance between colony and cargo ships. Would it be possible to set that taxation on a per type basis? Or is there some other way that balance has/will be adjusted?

Source, destination, stable still work as before, but destination is overridden if pressure is 10+

I don't want to go down the subsidize route again, as that could make the situation worse.

I am going to also add some changes to how civs decide what to build, based more on what is needed, but haven't got around to that yet.

Interesting changes! Not sure if I should continue discussing here, or move to the change discussion thread, but since we're here...

Will we still be able to set colonies as source or destination or stable?

Also, would it be possible to set taxation on shipping to be negative i.e. to offer incentives to grow their fleet, particularly early on?

Lastly, the changes don't seem to address the balance between colony and cargo ships. Would it be possible to set that taxation on a per type basis? Or is there some other way that balance has/will be adjusted?

2. Allow the player to determine (on the wealth tab) how much to tax colonist ship tonnage and cargo ship tonnage (individually). This would give players the flexibility to encourage or discourage growth by giving the CSLs more or less income and hence driving growth (and/or contraction if idea 1 were implemented). This would only require adding two numeric fields on the wealth tab, so hopefully minimal programming work.

Check the update I just posted

There was a bit more work involved though than just adding the extra UI elements.