My experience of cap ship combat is that one can be far more successful in a much shorter period of time commanding a destroyer or cruiser squadron than as a pilot. I ran through highlands as an attack fighter pilot, and found myself frustrated by the AI fleet command's strategic passivity and tactical idiocy, so after I got promoted to command rank I restarted and took command of the 66th desron in solus system. Using only the four ships in the squad, I was able quickly destroy the other three destroyer squadrons and take out the seperatist carrier group inside of 4 days and finish the campaign in 10 (it took a couple of days for the marrakan carrier fleet to show up and I actually had to move back from Renser space to finish it off at Jalah. The point (bragging aside

One tactical point that has been instrumental in my ability to successfully use cap ships is the practice of drawing enemy cap ship formations into suboptimal configurations by baiting them with one or two ships and stretching them out into a thin line. Enemy cap ship formations tend to stretch into a line with lighter units forward and heavier slower ones to the rear. When approaching a visually identified enemy, position your force to pass to one side or the other of the line (preferably to the rear of the enemy formation) at a shallow angle (say, 30-45 degrees to their line) and in emcon 2 or below. Once your lead ship breaks the plane of the enemy's axis of advance (i.e. when your lead ship is roughly in line with an imaginary line drawn through the enemies' ships, kick that ship up into emcon 3. This should get their attention. They'll usually flip ends and light off their main drives in an attempt to engage you. Since the lighter units are usually faster to accelerate, they'll tend to outdistance their heavier counterparts. Moreover, the necessity of switching direction and maneuvering to avoid one another usually results in them winding up strung out in a line. You'll need to have a little patience, maintain your heading and speed and allow some distance to develop between your ships and the enemies'. Once they are adequately spread out, engage the closest unit simultaneously with all your vessels, hopefully chewing it up quickly with multidirectional torpedo fire. If their point defense is good enough to prevent this, close with one or two units and disable pd or phalanx systems with your direct fire weapons (x-ray lasers or grasers). The key to quick, decisive engagements (which minimize damage to your ships) is concentration of fire on one vessel at a time while preventing the other ships from engaging. Failing this, position your flagship in such a way as to draw the majority of projectile fire, and try to maintain all of your torpedo-armed enemy contacts within your point defense envelope. Once the first ship falls, work your way down the line, making sure to strike each ship with overwhelming firepower from at least two angles. They can usually defend against torps from the front or rear, but they inevitably leave a flank undefended somewhere.
By the way, this is an exceptionally well done game, if destroyer studios could just manage to add some more human elements (crewmen, pilots, bridge officers) to manage I could finally remove the painfully disfunctional Universal Combat from my hard drive and get my complete starship command fix here. Anyway, sorry about the long post, I tend to ramble on.