Fleet battles should be more complex. One way of doing this is to make fleets larger, but not in flagship level, but making fleets be smaller fleets called battle groups.
The idea is to have a fleet able to split up and engage. Right now splitting a fleet isnt a viable combat option. Why waste time splitting your fleet to deal with another, when you can just engage him with the entire fleet?
Battle groups would be fleets within fleets. Each ship still has their flagship level, but a battle group level too, this would be a number similar to warp speeds. Say a 3/8 level would mean your fleet can have up to 3 battle groups, with 8 ships in each group.
Battleships and dreadnoughts would have the highest battle group level. A dread would have the same 18 flag level, but also a 6/10 battle group level. So you can have 6 battle groups with 10 ships each.
You cannot have your entire fleet engage one other fleet. You have to release each battle group to engage. If a enemy engages your entire fleet,
Your battle groups would come first. You can choose in which order the battle groups engage. If a battle group is destroyed by the enemy, another one will engage, i will talk about this more later. I should make this clear, IT SHOULD NOT BE POSSIBLE FOR AN ENEMY TO KNOW WHICH BATTLE GROUPS COME FIRST.
If a group is destroyed by an enemy, the next group will engage. IF they arent fast enough to enter warp. This is a part where i suggest speed values. Say, a battleship group would not be able to run from a frigate group. Or it would be on a ship size basis. Smaller ships will be able to catch bigger ships. So, having a full battleship fleet, a enemy battleship group can engage yours and be able to run away afterward. But, if you have destroyers or frigates in one of your groups, they would be able to catch the battleships and keep their group engaged. A fleet can travel as fast as the slowest ship. Id suggest that a dread would have a speed of 1, battleships 2, destroyers 3, frigates 4, corvettes 5. This is just a basic number but the idea is that a smaller ship can catch a bigger one.
Using this, you could potentially protect important ships in a hot zone. Say ammo ships or bombers.
Let me know what you think.