It would be nice if we could exclude known commercial ships from auto targeting or maybe even exclude them from the target list on the ship combat screen - only if we have the intelligence on those ships and know they're commercial of course.
Also, settings for construction speed and growth speed would be great (similar to Research Speed, Terraforming Speed, etc...) and being able to use fractional values for all the speeds available, example: I would love to reduce survey speed below 1% because even so it's too fast for my taste.