This is how I've always seen the freespace story line.
The Ancients were the original destroyers, in the first Ancient cutscene they talk about destroying and subjugating everything in their path.
The Vasudans are somewhat related to the Ancients, I am guessing that they were actually one of those subjugated, and forced to adapt the Ancient language.
The Ancients explore all the space they can, and own all of the known galaxy.
The Ancients create the knosses portal and create a great expanse of them and then they run into the Shivans, somewhere far beyond the nebula.
These portals are huge and in the game they say that it would take the Terrans years to make even one. So the network of portals setup beyond the nebula wouldn't have been done during a war. So the furthest portal is generally the last one they got up before they ran into the Shivans.
The Shivans send a massive fleet to destroy the Ancients.
This fleet includes more then 1 lucifer. Their worlds beyond GD are destroyed.
The Ancients taking heavy losses against the lucifer fleet disable the knosses portal going into GD.
However the node has stabalised as had happend with the GTVA. And so where they thought they would have stopped, a lucifer actually made it threw.
The home systems the Ancients talk about is everything on this side of GD that they owned.
During the fighting with the multiple lucifers they find out that it's shields don't work in subspace.
As the 2nd lucifer goes into the GD node the Ancients destroy it, and the node collapses. Cutting off the first lucifer fleet from the home systems.
However one lucifer is still on the GD side and has made its way to the ancients homeworld, the lucifer destroys it, and the ancients powerbase is destroyed. The lucifer has no opposition from that point on and destroys all the ancients systems.
The Vasudans have been freed and the Shivans are seen as their saviors, and that begins the legends of the comming of an all powerful race. (As a good thing not as a bad thing)
With all the ancients destroyed, which still takes the Shivan fleet ages because they don't know the systems on this side of GD and have to explore.
The Shivan fleet goes beyond Ross 128 looking for a way back, unfortunately there is none, there is only one jump node. So they head back to GD, unfortunately they run into the Terran and Vasudans and thus the great war begins.
The original Shivan fleet is out of date due to it's cut off from the main Shivan systems. At the time as the war with the Ancients shields on capital ships were thought as a good idea and beam weapons were new being tested on the newly designed lucifer class ships.
When the Ancients destroyed Lucifer 2 in the nebula-GD jump node, they collapsed the node. With this weakness of shields not working in subspace, any race knowing this weakness would engage the lucifers in subspace. Not willing to loose anymore nodes because of this, the Shivans stop putting shields on their capital ships hoping to reduce the amount of battles in subspace. Remember there is no portal on the nebula side of the node so the Shivans can't get it back up and running from their end.
They create a new design based on massive armour and weapons.
As for GTA technology advancing so fast, is only because of what they picked up off the Shivans during the Great War, if the Great War hadn't happend, the Terran-Vasudan fleets would have been only slightly more advanced then what they had in the great war, when the 2nd Shivan fleet would have attacked. Probably destroying all of the GTVA forces without them even knowing how to collapse a node.
I believe the Shivans unwilling to let any race exist ever again destroy the entire capella system instead of just the planets and would have continued on to do such at every system.