I think this is not a game where you are going to put half your fusion bombers on attack-move and half of them on hold fire, or whatever combination.
One of the reasons stems from unit churn: your units die and get rebuilt by the flagship, then come back into the fight with standing orders inherited from the flagship. So currently you really want to have the same standing orders for the whole fleet.
The other reason is just the pretty high level at which things happen in this game, micromanaging standing orders on five units in a corner just to have those orders potentially lost when you order the fleet around or they get killed just isn't worth your time.
Thoughts? Personally I'd like standing orders to be changed so they always apply to a whole fleet member group. So if you have one bomber and and one parasite selected, and change standing orders, those will be the standing orders for all bombers and parasites in the fleet.
With this change in place, standing orders can be inherited from what is assigned to the fleet member group instead of what is inherited from the flagship. This way all your parasites stay on hold fire to avoid getting slaughtered by turrets they can't hurt, and bombers keep cleaning up those turrets in full-on aggro mode.
The fleet panel would get an indication of which group has which order.
We could also go all the way and have standing orders apply to the whole fleet. It'd at least be consistent and easy to manage, but I feel like giving different orders to different unit types will come handy often enough to justify it.