Yeah, the autocast priorities need tweaking -- we should have mentioned that, but I guess we kinda assumed the devs knew that about all AI functions already.
Just to make sure I repeat:
Currently
all autocasting scripts are very bad and inferior to micromanaging.
A player that micros it's capital abilities will win easily over a player with equal capabilities, but who doesn't micromanage.
For some examples, the Dunovs shield restore ability is only useful for capital ships, but when used on them it can keep them alive for nearly forever.
The Kol's Gauss cannon (when you have 2 or even more Kols) can kill enemy capital ships easily (800 damage per shot). But for that, you have to have enough antimatter (since it costs 75 per shot). Which means you can never use the flak ability (doesn't do much damage to fighters/bombers anyway) and have to cast the shield ability manually (or your Kol autcasts it even when it doesn't get shot upon) and of course the gauss cannon ability itself (or the Kol wastes it on Kobalts and the like).
But you can't micro your Hoshikos and Command cruisers, simple because there are too many of them.
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The design of the Hoshiko makes it imho a repair ship. It's good at that. The command cruiser is a shield refiller, and it's also good at that. They are support ships which keep your fleet alive, ie. they should be stationed behind the fleet at best out of firing range of enemy ships (especially gauss cannons).
Now you introduce an attack capability to a defensive support vessel. Honestly that just doesn't work out. And that is why nobody wants to use the attack oriented capabilities, because nobody sees those two ships as attack ships. (At least, I don't know anybody how uses this ship for anything else then repair or shield refill.)
They have limited antimatter, so I want them to keep my fleet alive. Designate target costs like 100 antimatter. Antimatter I need to fill my ships shield. It gives an increase of 25% damage IIRC? That would be only useful against capital ships and to do that you need to deactivate the ability and micro it against capital ships. Boost morale on the other hand improves shield regeneration and boosts weapon cooldown by 10%, or in other words, 10% more damage for this ship.
The engine sabotage ability has a range of 3000, meaning when it's in range to do some damage, it's dead, since it's then in front of the fleet. I don't know how much slower it makes a ships, but even if it would force it to a standstill, it would only be useful against capital ships again. If I read the files correctly, it slows weapon reload by 0.75s, which is nothing.
Edit:
Frankly I think the Ceilo shield restore should be the tech for the Hoshiko, and give the Ceilo targetting ability a more general effect to the fleet; and give the Ceilo the timed explosive abillity as a upgrade.
Best solution imho. Because mixing offensive and defensive capabilities in one ship just doesn't work out.