Thankfully, there is a balance between the Super-Alpha1 syndrome and the opposite extreme of the player not having an effect on the battle.
The problem, as has come up often in this thread, is that if you have the BoE battles, there is no defensible reason not to have absolutely no reason not to have hundreds of fighters flying in support, which will cause problems for the engine. Think about it for a minute... if you have just two destroyers facing off, what possible reason would there be for their entire fighter complements not being launched? When a US Aircraft Carrier gets ready to smack something you better believe it puts up 100% of its fighter complement, leaving behind only the ones that just aren't going to be useful. For purposes of making realistic misssions that the player can play a pivotal role in, smaller battles are pretty much the way you have to go. if you have a BoE situation, then what needs to happen is that Alpha1 has mission requirements that he has to meet that don't nessecarily determine who wins or looses the battle. Surgical strikes against subsystems, weapons, and smaller ships, as well as protecting allied ships from bomber strikes are all good, especially under circumstances where there are plenty of other fighters around that are doing their own thing. In this instance, its simple enough just to use wings that don't accept player orders and have their own missions to run. Why should alpha wing be able to order around the bomber wings that are supposed to be taking out that cruiser and make them do something else?
slightly off topic, but in the similar vein of realism, I notice so frequently that situation where all the allied forces are destroyed/have left the battle, and there's an enemy ship that just sits there forever. How many of us have stayed behind to nuke some poor hapless shivan cap after a mission has actually ended just because we have trebs and there aren't any more scripted fighter wings helping it? If all the GTVA ships are gone, there's no reason for that moloch to sit there and take your beating. Make it jump out. I've gotten solo Demon and Ravana kills that way just by being patient and nuking something that can't fight back. Its just silly =P
So, in condensed form, this is what I think mission designers should keep in mind:
1: it is possible to make the player's role pivotal without making him responsible for winning the battle singlehanded. Destroying a key beam turret or protecting a key ship from attack is good.
2: Don't leave enemy ships hanging around after a mission has ended. It just looks messy =)
3: If you have multiple destroyers/lots of caps, remember that there should be lots of fighters to go with them. For every destroyer in a battle AT LEAST 50% of its maximum fighter/bomber complement should be in the battle or you should have a really good reason. (damaged/destroyed fighters, on missions somewhere else, etc). The exception to this obviously is when the mission shouldn't require more fighters then are actually present, but if the destroyer is in any danger of being destroyed, its fighters better be out there.