But the act of defeating it would have limited us to fighting an entire war in subspace had all shivan ships been fitted with it.
I personally got the impression that shielding an entire ship was a very difficult and 'expensive' thing to do, even for the Shivans, most of the Lucifers massive power went into that shield, hence the limited (compared to FS2) weaponary on it.
I cannot help but think that the Shivans would not go to the trouble of creating a ship like that unless it was something considerably more significant than a scout. It's not as if losses have ever really counted to Shivans at any other time, so why shield this one particular ship? Why, when we destroy this ship, at the next chance they get, do the Shivans send 80 Juggernauts against us, those Juggernauts must have been moving towards the system since, at best, the original Sathy first encountered the Colossus, but possibly even longer in my reckoning, I have a suspicion they were moving from the moment the Shivans first re-encountered the GTVA.
If these ships serve simply as warships, despite being very effective as one, then why are they in particular treated to added protection, especially since the shield on the Lucifer in FS1 was really the icing on the cake, and was mainly to prevent the player from doing something obvious like taking out the Beam Cannon

It's not as if the entire Terran fleet could have taken it down, shields or not. You would have thought that, if these are 'Blitzkreig' type vessels or even if they act like a Mobile Comm-node array, you would have seen some with the second Shivan fleet as well?
I can live with being a pawn when the game makes sense!
