Oh, so now what I think is irrelevant? Making statements like that is the fast track to getting a thread locked, buddy.
For the record, I'm well-aware that only two beams have to be destroyed for the mission to be a success. I also know that taking out all four beams makes the next mission much easier. In addition, I know it's very possible for all four beams to be taken out if you fly a near-flawless run; the challenge of that is what makes me replay that mission so many times. It's annoying as hell, but that's just part of the fun.
And yes, I don't think that the FS2 main campaign needs any changes. I say this because I think that there are few, if any, real bugs in it. I've played through it several times and never had any real problems with it, as, I would venture, have most of the people on this forum. You, on the other hand, seem to have a driving desire to completely change the main campaign, the main reason that the game exists in the first place. If you want to make so many changes, why not just create your own campaign, complete with weapons modified the way you want them to be? There's absolutely no need to go fooling around with the campaign, no matter what you may think. If you claim that the main campaign is that broken, give some evidence to back it up.
As a final note, I don't see how Trebs are "universe-contradicting." They're large, powerful, long-range warheads; why shouldn't they be able to do massive damage to subsystems? That makes perfect sense to me.