Pardon me if I don't get some specifics right as I have not played in a long time.
I realize I'm late to the game on this expansion but I've asked for this feature before. I want to bring it up again. Could ships protect each other with countermeasures\weapons? This would give us reason to design several types of ships for a task force, as it will make sense to specialize. You could then design task forces with specialized ships designed to work together, instead of alone.
For instance, a Carrier group.
3 Large Carriers, packed with fighter bays, a few point defence systems.
10 small fast ships, packed with point defence and short range weapons. These are there to protect the carriers from incoming fighters and missles.
The point defence ships will then form a ring around the carriers. The fighters protect the PD ships. The PD ships protect the carriers. They should move together in formation.
Just an idea that I think adds a cool strategic layer to the game. I hate how a missle flies by a ship and hits another one and the first ship does nothing.
Furthermore, I think it would be cool to be able to build an entire task force, from the production menu, instead of just individual ships. It could then automatically go to a single location and form up in a task force.
Just another idea.