But it also gives the benefit of deniability. If you tell the words through a possibly biased, or even possibly mistaken source, like the ancients, you can just rewrite the story later, without contradicting yourself.
I think that is just what

did. They changed how the Shivans acted, or rather why they acted in FS2 and if someone said "But in FS1 it was told that the Shivans are like this and that, so it makes no sense for them doing X and Y in FS2!", they can just say that the cutscenes only showed what the Ancients (or the single Ancients who made the recordings at any rate) believed, not how the Shivans really are.
In my eyes, the fact that the Shivans stopped at Capella, instead of immediately sending their 80 Sath' onwards to wipe out the GTVA shows that there is more, or something completely different, going on with them than just "destroying the destroyers" and thus proved the views the Ancients expressed in their cutscenes wrong or at least incomplete.
And a good change it was too, I think. "Kill them all" is just such a flat and boring goal for an enemy, better to have them mysterious like the FS2 Shivans and keeping the player wondering what they'll do and why, untill short before the end.