Throughout my reading of Scythe and Thunderhead, a recurring theme is that in humans, absolute power corrupts absolutely. This theme is personified throughout the books by Scythe Goddard, the martyr for the movement that is corrupting the ideals held by scythes throughout the books. Goddard is shown in the first book as one who bends the few rules that Scythes in the universe are forced to abide by just shy of breaking them. His idea for the Scythedom is that the systems put in place to limit Scythes from becoming what we would call "murderers", are just limits upon them. He wishes to remove all semblance of order from the system, and allow all Scythes to simply kill at their leisure. Killing as few or as many as they wish.
The foil character for Goddard throughout these books is Scythe Anastasia. Despite being a new Scythe, only being ordained at the end of the first book, she stands by those that want to keep the old ways, insisting that the rules and traditions put in place by the founders are the only things that keep the Scythedom pure. Anastasia and the Scythes with whom she shares common ideals are the exemplary scythes inside of her Scythedom. They are able to exist with practically unlimited power in their world, and yet they strive to live by the ideals set forth by the founders.
This theme and themes like it are recurrent throughout the books, with struggles between those who would keep the ideals of the founders, and those who would abolish them. It is the clearest example of a motif through all of the books I have read.