You know, when we are not talking about Star Trek styled pleb science, the wars in space take a whole another shade. Space war is more like a gigantic stealth submarine skirmish campaign, only that there are hundreds of submarines on both sides. This would happen in reality and reality is kinda boring, but pleb science may insult anyone who knows even a little about science, but it is very awesome to watch. So there must be a compromise between entertaining pleb science and sweet realism.
For that you should develop a an event based engagement mechanic. Basically the entire battle is reduced to ticks. Ticks are instant events within the battle engagement where the honey is located. One event could be where your forces engage enemy head on in very close range. Another event could be a firefight of scouting spy ships. Another event could be an ambush. As far as events are concerned, the edge of the universe is your limit. Event is basically a single battle within a greater battle. After each single battle, forces retreat to plan their next move. The time between the ticks creates the impression that the the sides plan and do their positioning for the next battle during that.
You could also tie in more than two sides. Just take your two sided events and let them happen to any two sides of engagement. Enemy 1 vs Enemy 2. Enemy 1 vs Enemy 3. Enemy 3 vs Enemy 18. Etc. You can also write events that happen when when three sides are present.
This opens up the ability to issue war doctrines. Doctrines would make certain battle events more likely. If your empire is all about boarding, you could issue a boarding doctrine. Your troops would suffer less damage from boarding and the boarding event would happen more likely. Yet again, if player's enemy issued anti-boarding doctrine, player's specialization would be useless and player would have to change one's doctrine...or the player could just churn more cannon meat at the enemy.
This would also enable sides to retreat from battles. Of course this would make an opening for the escape events.