I know it's a bit of a stretch but I want to suggest it anyway. The whole standing order section could be done away with if we just had a programmming style "if (<CONDITION>) GOTO <LINE X>" command in the fleet movement GUI. Combined with the ability to template, it would make it much easier to manage and optimize fleet movements.
A cycle is already implemented there, so why not make it a full queue with dynamic command ordering? Though again I do know this is a lot of work especially since it needs gui features I haven't seen implemented anywhere in the game. I hope it is still a nice idea to think about.
For example a scouting ship would be:
1: If (fuel lower than 50%) GOTO 9
2: If (supplies lower than 20%) GOTO 7
3: If (survey nearest body) GOTO 1
4: If (move to system requiring Geosurveying) GOTO 1
5: GOTO 11
6: GOTO 1
7: Resupply at nearest colony
8: GOTO 1
9: Refuel at nearest colony
10: GOTO 1
11: DONE
No need for GOTO's though, you could do this instead:
1: IF (fuel lower than 50%) THEN (refuel at nearest colony)
2: IF (supplies lower than 20%) THEN (resupply at nearest colony)
3: IF (true) THEN (survey nearest location)
4: IF (true) THEN (move to system requiring geo-survey)
and just evaluate them one by one each tick.