See also Request: keys to communicate with all combatants/all noncombatants in squadron. I implemented the best XML solution I could in Com Groups, but it's still not as convenient as dedicated keys.

Also, ordering multiple autons to return at once will make Cargo bay can be overfilled when autons return come up more often. I addressed this for ordering one auton at a time in Improved Auton Bay Screens, as well as making them relaunch on return if the cargo bay gets filled in between when they receive the order and when they arrive. Maybe these changes to the auton base class should be moved to core.

However this requires searching the system for autons, so I implemented it in a different and more efficient way when ordering many autons at once in Com Groups. This could be hard-coded, or you could split the difference by making the individual return command check a playership variable for data about what autons are in the system and which are already returning, but update that data if it hasn't been updated this tick, similar to the way I create the escort lists in Com Groups.

Edit: This pull request addresses the issue, storing the data on the sender object for efficiency.

Also, is there a particular reason that most commands only work while the ship is escorting? Is there any reason they couldn't go directly between waiting, attacking, exploring, returning, etc.?

This is slightly better in 1.9 Beta 4 because you can Ctrl+Click on multiple autons and order them. In the future, though, we should have a way to define subgroups and access them via hotkey.