Not sure if it's been suggested already, but it would be nice to be able to queue up orders that stay after an overhaul order. For example, when a survey ship completes a system, what I like to do is say Return to colony -> Refuel -> Resupply -> Overhaul -> Standard Transit through Unexplored Jump Point #2, for example. This way, I don't have to come back to that survey ship and it will simply resume surveying the next unexplored location once the overhaul completes.
Currently, it appears all orders are automatically cancelled once overhaul begins, so when overhaul completes I now have to revisit fleets to again order them to explore a new system.
EDIT: Similar request for when tractoring ships. Sometimes my survey ships run out of fuel before reaching a refuel point, I set my tug fleet to go out, tractor the survey ship, then release the survey ship back at the colony. However, once the tugs first tractor the survey ship, the order to tow the tractored ships back to the colony and release them is removed from the tugs orders, so I have to go back in and tell it to do so again.