I came up with two more questions Goober, hope that's okay (you could take it that people engaging in dialogue about your campaign means it's really cool):
Indeed it is. And yes, I take it in that spirit.
1-This is a response to your recent response to my previous question:
Why would they think it wouldn't deviate from attacking the planet? That seems like a risky assumption to assume a ship wouldn't make a slight maneuver since they know ships can move. In a similar vein, wouldn't it have been better to park the Legion behind the Lucifer instead of to the side which is in close view of its planet cannon? I understand you had to place it the Legion there though because that's where it was in the FS2 cutscene.
The Lucifer had already attacked two planets previously, SR-5 (in Ross 128) and Ribos IV. In both cases, once it reached its target orbit, it followed its pattern of bombarding the surface and did nothing else until the bombardment was complete. (Reference the mission briefing, which says "We do not believe the Lucifer will leave orbit until it has devastated most of the surface with its flux cannon weaponry. In previous engagements, the Lucifer has demonstrated unwavering focus on its primary mission objective, its shielding system allowing it to shrug off any distraction.")
Either the Lucifer needed to route all available power to the planetary bombardment beam, or it takes a bit of time to reconfigure from "planetary bombardment mode" to "capital ship attack mode". Note that in the mission, the Lucifer stops bombarding the planet after its reactor is destroyed. Furthermore, it doesn't attack the Guardian right away; it sits there doing nothing for several minutes.
The GTI expected the Lucifer to do exactly what it had done in previous engagements. In both previous occasions, it a) did not deviate from its orbit, b) used its forward beam cannons for attacking warships and its side beam cannons for attacking planets, c) did nothing else while it was bombarding the planet. But the GTI failed to consider that the destruction of a reactor might provide sufficient incentive for the Lucifer to alter its behavior. It may be single-minded, but it's not stupid.
Both the Legion and the Guardian were positioned out of the firing arc of the Lucifer's forward cannons, which is where the GTI assumed that any attack would originate, if the Lucifer decided to switch from "planetary bombardment mode" to "warship attack mode". They also assumed they would have a bit of warning if this were to happen.
2-This question kind of is about the final mission but also about FS in general:
The FS wiki says that while Helioses do much more damage to an overall target, Harbingers are much more effective at destroying subsystems/parts of a ship. Does that mean if a shielded Lucifer came back in the FS2/post-FS2 era and heavy enough bombs can damage it, the GTVA would be better served to bring back Harbingers rather than use Helioses?
I suppose, but neither Harbingers nor Helioses are particularly effective when the Lucifer's shield is operating. The overriding factor is the shield penetration ability. If the Helios is good at penetrating shields, it may inflict more subsystem damage despite being less effective against subsystems on unshielded craft. This is the sort of thing that would be up to the mod designer. The ideal strategy, of course, would be to use beams, against which shields offer no protection.
By the way, The Scroll of Atankharzim, Part I features the arrival of a Lucifer-class destroyer in the post-FS2 era. Though Sesquipedalian and I hold different opinions on what precisely happens when all five reactors are destroyed and the ship is not traveling through subspace.