(1) would be great as long as the limit remains one ship per tug. I'm not sure how much work it would be to code, but something similar exists for squadron jumping so it's certainly possible.
(2) Isn't really needed. You can detach a subfleet from a fleet into its own fleet and then have it rejoin later with the "Rejoin as Subfleet" order. Presently this is necessary since Aurora is coded so that every separate formation on the tactical map is a "fleet" and fleets don't have a hierarchy of fleets under them. However, the one reason I can think of why this would be needed would be if you have a flag bridge and want your ships to keep the bonus from that officer when they split off. Maybe a good way to implement this would be that a flag bridge functions like a naval admin command?
(3) I'm not sure what really needs to be added here. Currently we have the ability to ban civilian traffic from a body, civilian shipping as far as I know will not ship infrastructure and colonists to a colony that doesn't already have such things (e. g. a listening post or xenoarcheology dig), and CMCs as far as I know will not establish themselves on any body that already has a racial colony even if the colony is empty. These functions seem adequate to control civilian behavior pretty reliably as-is.
With regards to 2, I hadn't thought about that, but it's somewhat annoying to have either to a) constantly split and merge fleet containing multiple survey ships if you want them to hit multiple targets at once or if you have two classes of ship and some only work for geosurvey while others only work for gravsurvey but you want them organised into a single fleet most of the time so they can all be sent to different systems together, but split them up every new system to run the survey. Presuming you've got the standing orders set, you'll be ordering them to split and merge every time you move system. Being able to use sub-fleets as separate manoeuvre entities would be a big help, even if when tugging a station or damaged ship the entity gets made into a sub-fleet, it'll mean we keep the existing structure and don't have to keep remaking it if things happen or if you need things to move on their own rather than with their assigned fleet.
There's also, as mentioned, point b) You've a station group you want to use together, but from what I've seen as soon as a tug tractors a station, it'll make that station its own fleet meaning you're constantly having to reorganise when you've got stations running mining, fuel gathering, maintenance, terraforming, etc and you need to move them around to a new locale. (Luna finishes terraforming, move stations to Mars, Venus, Mercury, etc or Jupiter is out of Sorium, shunt the fuel harvester station group to Saturn, Uranus, Neptune or some outsystem gas giant without losing their grouping).
On point 3, the issue I've found is more for arch digs in that as soon as you have a construction ground unit dig up a working civ building, it turns it from a dig to a hab world at which point, particularly if the building is 'x infrastructure', civilian colony ships jump in and deliver population, which you might not want and might not realise until you check the eco screen. Yes you can tell the civvies not to have anything to do with a colony, but when there's a change due to an event, if you're not checking things when you set a colony, you can wind up having the AI screw you up, particularly if the dig is a high cost planet like Venus, or one you never want colonised even if it's 'viable'. The other thing for automines is more a visual aid. Most colonies we create start as 'other' unless they've got a ruin on site, but auto-mine sites change colour in the fleet orders menu, and shuffle around if you've got 'view by role' on the eco screen, allowing a quick reference for where you're aiming to actually colonise/terraform versus where you just want mines
prior to sending anything there, particularly if it's something that might take a while to do because you've got to build things first.
It doesn't even need to be much, just allow us to decide
without dropping anything what body has a particular classification of colony and don't auto-change it. Space Empires IV and V allowed you to pick a colony type as a player, so just letting us set and reassign so we keep digs as digs and can see our locales for mines/pops if we have to return to things later and have forgotten what's supposed to be what would help.
