Ships and task groups should automate refueling.
(sorry if this is a repeat suggestion)
The role the player plays in the game is one of a fleet admiral directing an entire fleet. The fleet admiral normally doesn't have to tell a ship captain to make sure his ship is refueled and supplied. Its the responsibility of the captain to make sure his ship is ready to perform its missions, and this includes making sure the ship is fueled and supplied. The admiral might occasionally give an order to make sure all tg's in an important mission are refueled and resupplied before they leave, but the fleet admiral isn't constantly going to be telling his captains which gas station to go visit and how often. As such, I'd suggest automating the refueling and resupply of ships and task groups to the extend possible.
1) A ship or task group that is at the same location as a refueling source (colony, tanker ship) will automatically top up on fuel given the opportunity. The same for resupply sources and re-ammo sources. A ship's captain or tg commander is always going to grab the supplies he can for his ship at any opportunity.
2) The conditional-type orders on a tg now flip around. Since the tg commander is assumed to be looking for chances to resupply, refuel, rearm, the conditional orders available set limits on this. One conditional order would prohibit these action. Another conditional order would set a max range of how far the tg will travel to go re-up. The range can either be a distance within a system, or a number of systems to travel to re-up on logistics.
3) distribution of supplies and fuel within a tg should happen automatically. A tg commander isn't going to let a ship run out of fuel, then call home to ask what to do about it. If any ship drops below a certain fuel level, it should get refueled by its tg ships. In case of emergency systems failures, it should be possible to transfer supplies between ships to avoid having a component fail. For that matter, it should be possible to do damage control within a tg even if the ship can't store that many supplies. Who cares if the parts to fix the broken thingy came from a locker on this ship or were shuttled over from another ship in the tg.
4) The player should have the ability to either 'turn off' or set a reserve value on logistics sources. Thus, a colony might always be told to keep a million gallon reserve of fuel, and when that limit is reached it stops refueling ships. Also, you could have the concept of military and civilian supply depots. If a supply source is set to military only, the commercial ships won't resupply there.
This way, there's a loop that happens regularly(presumably when conditional orders are now checked?) that where each tg checks for supplies within the range that's set for the ship. If it sees an allowable supply source within that range (which can be zero), it automatically re-ups on fuel, supplies and ammo.
Example, you have a task group patrolling at a jump point in a system, but set to resupply from supply sources within the system. You then send a ship with fuel and tanker status into the system. The tg commander sees the opportunity to top-up his fuel reserves and gladly takes it. He flies his TG over to the tanker, refuels, then flies back. If as fleet admiral you don't want the tg leaving its post for even a short while, set its 'logistics range' to 0. Then, if you order the tanker to fly to the tg's location, the tg commander will then gladly refuel, but the TG won't leave its post to travel to the tanker. If as fleet admiral you don't want the tanker to refuel the local units as it flies off to another important mission, you could give orders to 'turn off' its tanker status until it gets where you want it to go.
This way, the game is less micro-managy for the player, and it simulates at least what our real-world simian race does which is to have a military that's full of scroungers looking to grab whatever they can for their unit.