Also, at this time, there is very little micro management in sins rebellion, adding this would not be over the top. It would be basically the click of two buttons, maybe some tab action in there somewhere. If the different ship types moved in groups you could target by groups or ship type. This really isn't that hard.
If you don't micro manage ships in this version of sins, Well it is safe to assume you have trouble beating 1 unfair AI fighting against you. This game as it is not click fest as starcraft is needs a lot of micromanagement of battles. That chasm divides skilled players and not so skilled.
To know when it is worth to Focus fire capital ship or which type of ship to shoot at with which positioning of ships relative to friendly and enemy ships in battle. When to retreat ships, when to jump reinforcements in which abilities use and when to use them ....... all those things make sins easy game to play and hard to master. And believe me it takes a lot of micro which would end up being impossible by adding dynamic movement.
PS There exists a mod that adds dynamic movements to ships. Try it out. It could work for you because you just let ships fight on their own. For people like me who try to constantly issue orders to tip the scale into our favour by using weaker fleets to destroy stronger. It doesn't work.