You seem to be forgetting about one other empire the Shivans annihilated - the Ancients. It's safe to assume they were quite more advanced than the GTVA during the Second Incursion, yet they were exterminated in a matter of what, weeks, months?
I'm not sure if the Ancients were much more advanced than the GTVA by the end of Freespace 2, or even if they were more advanced at all. The Ancients were able to build Knossos portals, but they couldn't build beam cannons like the GTVA, or communicate with the Shivans like the NTF, for e.g. Considering that the only tech we know they had that the GTVA didn't was the Knossos portals, and that the GTVA eventually learns to build them, it's likely that the GTVA surpassed the Ancients technologically by the end of Freespace 2.
Allow me to bring up another Ancient cutscene, the fifth. 'The destroyers that darkened our skies like a plague can be harmed.' How many destroyers did the GTA and PVN fight during the Great War? 1 Lucifer and 2 or 3 Demons? Going by that, the Ancients were being attacked by dozens or hundreds of Lucifers, plus who knows how many other capships and their fighter complement.
I must ask something regarding beamz. I've only played 3 campaigns that involved an attack on a Lucifer, other than FS 1. In Awakenings, they used the Pandora's Box to magically (magically meaning I don't remember what they did, some sort of subspace explosion I believe) disable the Lucifer's shield, so that it can be attacked by laser turrets. In Derelict, we have the Nyarlathotep (did I get it right?), an unshielded Lucifer that has regenerative abilities, I guess this one doesn't count. And in AoA you don't get a Lucifer icon when targeting it, but we all know what that impenetrable shield really is, an invulnerable flag. Back to the point, did some Faustus-class SCs discover some sort of fluctuation when the SSL penetrated the shield, or what exactly led them to the belief/certainty that building a 6 km bat equipped with 13 beam cannons would protect the GTVA from a future Lucifer threat?
I only asked that because Valrog assumed the Ancients lacked beam technology, while I assume there's no reason they wouldn't have developped it. They were either outgunned or they may have only discovered it, and they weren't powerful enough, there's any number of theories.
One more question: Do you know what plot holes are? Because, IMO, using one as an argument is seriously not a good idea (ETAK device). Sorry for bringing Mass Effect back in, but the same thing happens in both. Super-advanced aliens encounter more advanced alien life, are exterminated by it then most proof of their existence is destroyed. Some remains of the Protheans were discovered, that VI I can't name right now, just as some data remained after the Ancient massacre, information on how to defeat the Lucifer and the location and activation codes for the Knossos device, and that's only what the player was told about. There's no proof the Ancients were incapable of building their own version of ETAK, but there is proof they
would not have attempted to. Ancient cutscenes again: 'Ours was a proud people, and always the strongest.' ; 'When the destroyers came for us, we attacked. Never had we been defeated. They are like the others. Strange, hideous, resisting, fighting.'
Ok, I rambled enough.