Ok I know that the dreams of a ship combat system where we give ships orders and fight out a battle and everything are not gonna happen. Yes its sad I know (at least for some of us). However, I strongly believe that having the only user input into the combat process be what ships are present and what their designs are is not nearly sufficient. Personally, I really like to feel like I have some hand in the battle itself. Therefore I have come up with this idea:
When a battle takes place a new screen pops up and displays info on each fleet. Then the player can choose from a list of strategies. Each option will have different advantages and disadvantages and will be more or less effective against other strategies. The player will not know what choice his opponent will take. Then once the player selects one he clicks a button and the battle is resolved based on the regular combat abilities of the fleets and also the strategies chosen. This way we can have some input into how our fleets fight.
Examples of strategies might be something like:
all out attack: large bonus to attack values, large minus to defense values
defensive formation: inverse of above
standard: just use the normal values