I think we've discussed "standing orders" before. I found them really useful in games like xconq and ultracorps. The basic idea is that a system can have an order assigned for each type of ship, either when it is produced, or maybe just whenever it enters the system. This makes it easy to generate supply lines and factories without scripts, although when enemies start capturing parts of your machinery it is a pain to recover.
This might not work as well in this game if ships had to decelerate and arrive at a system to receive orders. IIRC UltraCorps only had standing orders for production, but that was still pretty useful.
Also xconq didn't have a "fleet" concept so that makes it simpler. I don't think UltraCorp did either really: my memory was ships were either in-system or in-transit: whoever was in-system functioned as a fleet, and in-transit they were simply untouchable.