AoA played in a parallel universe. We don't know wether the fights over there have any influence on the GTVA/UEF universe.
And from a certain point of view the Shivans always were the good guys. They wipe out those that would kill the weaker species, so they can flourish.
Do you consider the people who almost wiped out the wolves in Europe in the past evil? They were doing what they thought was necessary to safe their families after all, no matter that their judgement was based on wrong information. For the Shivans we are the wolves and the species to come are their children - untill they in turn become the wolves.
Good and evil, morality, justice.... it all depends on point of view. What for one person is a sin, is a virtue for another (like killing unbeliefers for example... or killing wolves). A very cynical person could even say that such concepts as good, evil and moral are just a way to force your own ideals onto others. Make everyone the same and chocke off individualism.
That there is no definate good and evil in Blue Planet is one of the things tha apeal to me so much. Instead of saying "we are good. shivans are evil" or "UEF good, GTVA evil" all sides have valid reasons for what they do. It provokes thinking about and discussion the situations and points of view of each side.
They're murdering monsters.
What did the Shivans do? Massmurder, indisciminate killings and genocide. And all that towards some purpose, not for fun.
Humankind? Massmurder, genocide, indiscriminate killings, torture, rape, use of weapons with horrific aftereffects (nuclear bombs, chemical weapons, napalm,....). And all that for petty matters or even for pleasure.
If there are murdering monsters lose in this universe, I fear they are us. And looking back at our history makes one wonder if the Shivans arn't justified in wiping us out to make room for a better species.
On the other hand, there always were, and hopefully always will be, those of us who don't go that path, which might make us worth saving.