This post reminded me of an article by Cal Newport, in which he discusses the curious work habits of a famous mathematician. A good read:
You Can Be Busy or Remarkable — But Not Both - Study Hacks - Cal Newport
It's easy to create a dichotomy between busy work and innovation/deep work. Busy work can be a pain, but it's often a necessity: there's no justification for avoiding your long list of process-related to-do items if they just need to get done.
That said, I think organizational innovation is a function of making time for uninterrupted and unstructured thinking. One thing that helps me here: do a regular weekly review every Friday. Scrutinize the projects that you completed that week. Identify ways in which you were effective and efficient; dissect the mistakes that you made (perhaps using the Five Whys method: 5 Whys - Wikipedia, the free encyclopedia); and write down how you can do better -- i.e., how you yourself can innovate. In my experience, I've found that there's no substitute for this kind of strict introspection.