My first suggestion is to allow the player to flag fighters and frigate-class vessels as an interceptor/pursuit detachment. This detachment would break off from the main body of the fleet and engage fleeing enemy fleets, as long as they fall within a certain maximum pursuit range. Certain ship classes and modules could potentially extend this range. When the interceptor detachment catches up to the enemy, battle is joined immediately. Only ships which comprise the detachment are available immediately, and the main body of the fleet is placed in reserve. Unlike normal reserve, the main body can't be called in as reinforcements until a variable amount of time has passed, the duration of which is a function of the size/speed of the main body and the distance it was from the detachment when battle was joined.
Another thought -- I don't see why a ship's size/mass should influence its maximum speed -- it should only affect its acceleration. My second suggestion would be to make larger fleets with heavier ship classes simply take longer to achieve a uniform maximum speed -- a top speed which would be shared by fleets of any composition. Small fleets of frigates should handle like sports cars, in that they should accelerate quickly to top speed and turn relatively fast. Larger fleets should handle like an old Buick -- they should take longer to get going, and turn more slowly, but they should have about the same top speed.
I'd also love to see a new panzerschiff/"pocket battleship" class of ships that are faster than anything bigger, and outgun anything smaller. These would be destroyer-sized hulls with large mounts instead of medium, low crew requirements and cargo capacity, and higher-than-average fuel capacity.