First off, the anti-fighter weapons avaible to cruisers should be made defensive in the same way the anti-missile defenses are. What I mean is they should be treated as an entirely different set of weapons from the rest, just lite the anti-missiles weapons do. As it is now leaves a weird situation of you cruiser either trying to hit fighters with heavy plasma and anti-fighter or trying to a cruiser with anti-fighter and plasma. See my point here? Make the anti-fighter weapons independently functioning lite the anti-missile deal.
Secondly I think it would add a great deal of depth if you could plot courses for your fleet, or at least give them a generic “all ahead full” or “hold the line” orders. I’m not talking about anything major here, just give the fleet/individual ships som waypoints to go to during the fight. Many times my fleet has just freaked out and remained imobile in the center even though there are long range weapon pounding them. At this point I wish i could’ve either planned a route for them in advance or given them a general order of just moving towards the enemy/opposite edge of the map if they have nothing better to do.
Otherwise, awesome game, love everything about it so far!