The auton bay randomly picks which auton in your hold it repairs each repair tick. It also has slower repairs for higher level armor than low.

This would be fine, except in the later game there's usually no other way to repair your autons. And if you're running a swarm with high level armor, especially a large one and have a bad battle, you can then be sitting for a very long time. On my current autons-only run (which is to be fair an extreme case - I am running in excess of thirty moderate to high level autons at once) I have had multiple instances of having to sit on autopilot for over fifteen minutes to get things up and running again, even using manual armor swaps on some autons to speed things up. These long repair times started even in the UT, and have become a regular problem in the Outer Realm.

I'm not sure what the solution to this is. Commercial auton services could work if they were available outside of auton dealers, but those aren't implemented yet. A higher level auton bay could work as well, as would a standalone device that improves auton repairs... but then you need to be able to get it. I don't have anything conclusive, other than that the current repair times are simply too long at high levels. Yes, my way of using autons is unusual, but even with smaller swarms the wait times will get excessive if you use the auton bay the way it's intended, rather than ditching it partway through the game entirely. We can't have players sitting on autopilot for even five minutes waiting for repairs, and at this rate I'm looking at possibly as high as a thirty minute wait if my entire swarm needs to be rebuilt after a bad battle.