My personal thought on BoE missions is that FS isn't supposed to deal with that kind of stuff unless your tables are balanced enough to make it work. I'm refering to beam cannons, that turn immense battles into chaotic ones.
IMO BoEish missions could work if:
a) There are no beams and warships use heavy turrets/railguns to battle each other. This prevents insanely loud sounds, makes flying safer(no risk to get fried by a beam);
b) You're using a mod with altered game Physics for spacecraft. In many tests I noticed that spacecraft with high speeds&inertia turn certain missions into very interesting ones. I've also noticed that they last longer in combat. Obviously, all anti-spacecraft weapons need to be balanced to deal with the changes;
c) Overall the anti-spacecraft and anti-warship capabilities of all ships are balanced enough to make sure that spacecraft and warships last long during the battle, without any overkills. That's one more reason to drop the usage of beams;
d) There are no exaggerately big wings(or there are only a few of them) being sortied to fight. I think small wings of 2-3 bombers or 3-4 fighters at max are more balanced than immense wings of 6 fighters/bombers;
e) Warships aren't ordered to attack each other but rather follow certain waypoints paths at a certain speed. If you order a warship, especially a big one, to attack another warships odd results will surely occur;
f) Ships should be wisely disposed on the battlefield. Don't forget the Y axis and don't concentrate all ships in a small area;
g) Major battles could be possible with a better AI, at least for spacecraft(since ordering warships to follow waypoints solves most problems). Think about bomber wings opening their formations to ensure the success of their runs or stuff like that...it'd make the difference;
Although I consider Zarathud and Karajorma's thought on BoE as the Words of God I think we can make some exceptions by considering certain environments - like the ones I mentioned above - in which BoE concepts would work.
In addition, I prefer to use the concept of "Encounter". That's how I define a compromise between a normal mission and a BoE one...there are many ships but their disposal, weaponry, hitpoints, etc. etc. make sure that missions don't end up with a BoE battle.
Another important thing I'd like to say is about the role of the player. In my opinion the player isn't necessarily supposed to turn the tide of the battle but he can, in certain situations, be some sort of "visitor" or " active observer of the events". For me, it's important to let the player realize he can't do what's needed to save the day and that a single fighter/bomber isn't enough to change the doom of a fleet. I like that sort of feeling...
Also, please note that the objective of a BoE style mission may not necessarily be "Crush the entire enemy fleet": the player may have to protect a certain ship nearing the battle, acquiring informations by scanning ships or in other ways, etc. etc.