I find myself amazed at how elegant the Hideuze look in a mathematical sense (the Golden Spiral) and I can't have been the only one who caught the the Alliance has the Vitruvian Man as a symbol.
http://en.wikipedia.org/wiki/Vitruvian_Man
Count me in as someone who thinks the Alliance is the true "baddie" in this series. The way the Alliance essentially sleep indoctrinate their soldiers, and their use of eugenics in how they only allow a select few the privilege of breeding makes me very suspicious as to how much they are the aggressor in the conflict.
I do wonder how much Amy will change Ledo and how much Ledo will change the members of the Gargantia. I have a suspicion that the dark part of this from Urobuchi is how dark human nature can be, but I think this will end up happier than most people are expecting.