The brain states that earth was seeded, and they (They?) intend to harvest, so I guess that the aliens never really waged war on us - they (They?) were on a big supply mission. the alien soldiers we encountered were really just on a backwater mission to gather resources from one of the planets they seeded long ago.
This might explain why we actually had a chance of defeating them (Them?).
Did they (or They?) intend us to develop as far as we did, though? What is their usual regime for seeded planets? do they (They?) usually return after just a few centuries, harvesting biomatter? or is it normal for them (Them?) to wait until technological civilizations have developed, to also harvest refined materials from the planets? have they (They?) simply waited too long before returning to earth, so that they faced a rebellious group of more-or-less intelligent and more-or-less advanced ape-descendants that were determined enough to fight and defeat them?
perhaps there really is a huge-scale interstellar war raging, and they (They?) were distracted. when the war started to turn against them (Them?), they tried to gather what resources they (They?) could, and returned to the small blue planet which they (They?) had seeded long ago.