Ejection seats (well it has been done, kind of - ask Colonel Dekker about his eject-o-land mod).
Indicators on the HUD that highlight the position of incoming missiles (like a targeting bracket but for missiles, with range to missile also indicated). Actually I remember a thread about this being mentioned a long while ago, someone had apparently made this possible. You'd see these little yellow circles appear around the missiles. It would look cool if someone launched hornets at you.
Making capships block the missile's line of sight when trying to obtain a lock - might not be a good idea but it would be a bit more realistic IMO.
One or two model issues: Aeolus - is it me or does it have beam cannons on its sides that look like huge missile launchers? Also I think the Hecate has anti-fighter beams on its frontal "fins" that look like missile launchers too, I just don't think it looks right. Whilst I'm on the subject - making those stubby beam cannon turrets like those on the Orion turn and track targets... Would probably require new, multi-part turrets or something. But I can live without these changes.
Hmm, I'll go away and try to think of some more.