The biggest problem I see with the "Shivans were created a long time ago as destroyers and have been blasting civilizations ever since" is that it doesn't explain why the Ancients were able to form a vast empire and conquer other races (which must have been the work of centuries if not millennia), while the Terrans and Vasudans got noticed by the Shivans much more quickly.
And yes, I'm aware that the Historian timeline has the same problem. 
The best I've got ATM basically boils down to "the ancients got lucky lol."
This puzzles me too.
Though it can be explained, 1st by Ancients first having an empire, and only then discovering subspace, as we see in Great War campaign. So by the time they start subspace travel - they already have an empire. Also, amount of traffic, which goes through subspace is not that huge in the beginning, and then, when it comes to larger amounts, Ancients are detected by Shivans and annihilated.
As for Humans - after finishing Ancients empire, and seeing that they failed to detect it while it was relatively small, shivans made some improvements to their sensors - and so they response time to increasing subspace travel usage got smaller.
But still, having Shivans beaten by GTVA doesn't make sense at all, from this specific point of view. BluePlanet's idea of great destroyers and great preservers is way too mythical and mystical. So there must be some other way.
One of the ways is - shivans are currently occupied by annihilating another Ancients-size empire, so it was only a small "border guard" with one Lucifer which was spared to destroy Terrans and Vasudans.
