Okay, in regards to all of the speculation about what the Ancients WOULD do if they returned, it's fairly obvious.
Have you all forgotten about what we learned about the Ancients in FS1? They weren't a friendly race. They butchered and wiped out other smaller races. The fact that the Shivans got to them was just to show that there's always a bigger fish. Remember how in FS1, the Shivans were called the Great Destroyers, but also the Great Preservers? Had the Ancients remained, they would have butchered the Humans and Vasudans.
It's quite logical to assume that if they survived, they wouldn't treat the GTVA in a friendly manner. I'm assuming the whole point of Shivan return in FS2 (and maybe even in FS1) was to finish off the remaining Ancients.
Perhaps the Shivans sealed themselves off from the GTVA was simply to show that they had no interest in continuing fighting, and the fact that the GTVA was perhaps exploring into star systems that we shouldn't have been.
And, finally, let's not forget the second Knossos Portal that SOC finds. It clearly shows that the Ancients were located deeper within Shivan territory. It's logical to assume that the Ancients are not the 'good guys'.