One of the big conversation points a while ago was how this campaign fits the idea of the Shivans existing as both "Preservers and Destroyers" and how that fits in with the
Vishnans.
It seemed clear to me that...
The Shivans and the Vishnans aren't the lightside/darkside of the universe aimlessly bashing it out for control of the lesser races. The Vishnans seem more like teachers and educators, while the Shivans are the muscle that keep the galaxy in check. They BOTH want races on par with the old, creative Brahmans. The Shivans destroy those who fall into warlike existences, and thus preserve the potential of future races. This was explicitly mentioned in the second to last mission. These two factions are actually complementary to each other... until the Shivans overstepped their boundaries and duties by seeking to annihilate the Terrans and Vasudans after they put aside their differences to unite, both in the alternate universe and the primary GTVA one.
Obviously, many people hold their own canon on what they consider to be the future of Freespace. But what's in Blue Planet doesn't contradict anything in the canon of the first two games given what they tell us.