If the player can't do anything meaningful in a mission, then it's badly designed mission. If the player can't do anything because bazillion ships in the mission are killing his compootar, it's a BoE mission... If a battle is big, it doesn't necessary classify as BoE if the player has something interesting to do (tatical goal or sumthin'), and that the mission doesn't choke up on itself. There's a difference. At least IMHO.
Shadow war missions. How about protecting civillian evacuation during a major assault. By intercepting any stray spitfires, while main Shadow forces are doing something else.
Or testing an experimental bio warhead on Shadow ships. And then trying to evade the slicer on the pissed off battlecrab when the test fails (requires lots of scripting methinks).
Trying to figure how to kill a crippled Shadow ship in an 'roid field.
Fighting against people who have sided with the Shadows (like Centauri did).
I'm not telling you more. But with a bit of pen and paper time, I could propably come up with a sane campaign...