It's possible the GW Lucifer fleet is a remnant of the Shivan fleet that destroyed the Ancients, and ended up stuck on this side when the Gamma Draconis Knossos was shut down(perhaps with the Ancients' better knowledge of subspace, the Knossos could also be used somehow to close an unstable node faster than merely allowing it to decay naturally?).
Either the Gamma Draconis Knossos was shut down by someone, or it somehow shut itself down, as I doubt Bosch could have done much in terms of repairs had the portal simply run itself to death over hundreds or thousands of years, especially not without drawing attention to such operations. The fact that the second and third Knossos were still in operation seems to suggest to me that the Gamma Draconis Knossos was shut down on purpose, by someone.
To the best of my knowledge, we don't know exactly where the Ancients' homeworld was, but if it was in the Altair system, that is clear on the other side of the
official nodemap from Capella(and Gamma Draconis). Perhaps the Ancients tried to cut off the Shivans a bit too late, just as the GTVA did, though they may have succeeded in cutting off Shivan reinforcements, including the Sathani, or whatever else the Shivans may have been using at the time(while reasonably logical, perhaps, nothing explicitly says the Sathanas having uber-beam cannons is actually any part of the superjump technology, merely that the arms which have the cannons on them bend to generate what certainly appears to be a subspace warp opening).
If the Lucifer fleet is a remnant, it would also need to either find a way to 'sleep' or shut down for thousands of years, or(more realistically) start manufacturing parts or cannibalizing some of their ships to keep the others running. Societally, that has some interesting potential. The Lucifer fleet that the GTA and PVN run into, having lived apart from the rest of their kind for thousands of years, could/should be of a very different culture than the rest of the Shivans(the FS2-era Shivans). Throw in the fact that the canon Silent Threat campaign claims the GTI may have known of the Shivans before the Ross 128 massacre, and were studying Shivans at Jotenheim, at least since the Ross 128 massacre, and I imagine it's possible the GTI 'accidentally' poked the proverbial sleeping Lucifer fleet bear, and got way more than they bargained for.
FS2 could have been all one giant misunderstanding by everyone:
Bosch: Thinks we need an alliance with the Shivans, or else they'll destroy us when they come back.
GTVA(perhaps apart from the highest/higher levels of Command): Thinks the Shivans are a race of vicious, omnicidal xenophobes who can't be reasoned with, because of experience with an isolated group of their kind.
Shivans: Just want to go home, and as something like a race of ancient pseudo-eldrich abominations, really don't care about the puny Terrans/Vasudans, as long as they don't get in their way. Who says the GTC Vigilant or an escorting fighter didn't panic and fire the first shot, or otherwise do something that might have provoked them(intentionally or unintentionally)?
...okay, so they have awfully big guns for a civilization of not-really-warlike beings; maybe they prefer to put up a front to cow 'lesser' races by fear and intimidation(explaining their love of obviously evil-looking, pointy red-and-black-motif ships)?
Much later EDIT: So, yeah, I forgot about the CBAni depicting the Rakshasha beaming the Vigilant
seconds after jumping in(using totally incorrect beam arcs for the front beams), but technically,
their first contact was with the Trinity, not the Vigilant, so it's still open for debate.
Just had to correct myself in case someone came across this post in the future.