I think there should be a way to order certain classes of ships or groups of ships to concentrate on a certain kind of target.
I've been in several situations where it would've been useful to override the default behavior of certain units. Though I don't know the exact algorithm that determines how a ship chooses its targets, it seems to me that it's heavily influenced by what type of damage a ship's most powerful conventional (non-special ability) weapon does, and which targets are most vulnerable to that kind of damage, and in some cases, which targets are most valuable in terms of cost. This is why Hoshikos tend to attack and use demolition bots on light carriers, which isn't really as useful as using demo bots on heavy cruisers. The Hoshikos standard weapon is pretty weak, but it does do anti-heavy type damage. Of the types of ships with heavy armor, light carriers are the most valuable, thus the Hoshikos tend to pursue them the most. Sometimes, this is good. If the enemy's retreating, slowing his carriers down with demo bots so I can destroy them is good. If he's not retreating, I want to use the demo bots to disable the weapons on his heavy cruisers, and I want to be able to do that without having to individually order all my Hoshikos to use demo bots on all the other guy's HC's.
Similarly, interceptors tend to attack bombers because interceptors do anti-light damage and bombers have light armor. Normally, this is OK, but after your interceptors have pretty much smoked your enemy's bombers, they will continue to pursue stragglers (you can never kill every last one of them until the enemy's carriers are destroyed) while ignoring enemy LRFs and interceptors. So, similarly, I'd like to be able to order all my interceptors to start fighting enemy interceptors without individually giving focus fire orders on every enemy squadron.
These are just two examples. I have no doubt that there are other situations this would be useful. I know that sometimes I want my HC's to attack enemy HC's rather than go for enemy LRFs first. And so on.
And if we can't get this feature, then it'd help a lot if we could draw a box around units to attack kind of like you can do in Starcraft. Requires more micromanagement, but it would accomplish many of the same goals.