Is the development of an original/novel method a contribution to knowledge worthy of a PhD?
While developing a method has merit within science, that method needs to be useful to answer a question which is not currently answerable. I too have worked primarily on methods development in graduate school, and got stung by this in some of my early work. So, while it's good to focus on the method, always have the question in front of you: "what do we want to know, that we can't know yet, that my method will be able to tell us?"