If I had to distill Blindsight down to a single, central theme, it would be that of self. What is the concept of self? How does it relate to the concept of what is human? What is the origin, function, and cost of self-awareness? How does it relate to free will, and does free will exist, or is it merely an illusion? Watts seems to have created the entire novel as a thought experiment to explore these concepts, and he leverages two lenses to accomplish that: the various neuro-atypicalities of his characters, and the distinctively intelligent but unaware aliens. Either of these ideas alone could have easily been the foundation of a compelling novel. Combining them together made this one both more compelling, and more challenging, and is in many ways at the core of my personal dichotomy over Blindsight.
Creative writing, or the speculative fiction genre, has long leveraged something called the MICE quotient. I first came across this when I was reading an Orson Scott Card book on how to write science fiction and fantasy (I think it was even titled How to Write Science Fiction and Fantasy). The premise is that stories in the speculative fiction genre can be broadly binned as having one or more of four, primary drivers: milieu, idea, character, and event. Although most good stories will incorporate multiple of these components, with different ones emphasized at different times, there is usually one that drives the story forward.