Here is an excerpt from the Lucifer FS1 table file:
The Lucifer is the greatest threat to the survival of the GTA, the PVN, and both the Terran and Vasudan species. It wields three massive Flux Cannons which can destroy one of our capital ships in a few hits. These same cannons have been seen bombarding colonized worlds.
Now, we've seen no indication of 3 cannons of this type on the Lucifer, so this can be taken as not being entirely matching the game.
In the FS1 Reference bible (which also doesn't exactly match the game) there was a reference to the Vasudans possibly being an offspring-race of the Ancients, like seeded by them or something.
Personally, I'm going for the "Shivans go for the homeworld(s) first, then mop up the colonies afterwards" even if the table entry is accurate. If we wonder how the Shivans know which system is a species' homeworld, I'd point out that the Shivans have subspace tracking technology which is far superior to that of the Terrans and Vasudans, so they probably use it to track the subspace activity of those species and find out where its most active.
I'm guessing that very few of the Ancients would have survived the Shivan attack. In the final voiceover cutscenes, the narrator indicates that they had the capability to track the Shivans in subspace, and knew how to take them out, but had no means to launch the attack. That suggest that either A- their fighters had no inter-system subspace drives, and they had no cap-ship capable of transporting their fighters to initiate the strike, or B- they had no remaining combat craft whatsoever. I'm not a fan of A-, since we've seen that the Ancients indeed possessed advanced subspace tech even prior to their encounters with the Shivans, in the form of Knossos tech, which means that they likely had inter-system drives on their fighters. So, with no warships left, they'd have no way to cover any civilian ships trying to escape the system. If the Shivans had left their colony planets untouched, they'd likely have left ships behind to take out anything that might have got into space. The only way I could see any substantial Ancients' fleet assets having survived, is if a section of their fleet was cut off as the Shivan advance did a pincher attack to invade systems surrounding the central system, to prevent escape. Rather than coming to their civilization's defense, this Ancients fleet decided to do the BSG thing and make a run for it. In doing so, the fleet managed to get outside the Shivans' detection threshold.