Fast Cycle Change in Knowledge-Based Organizations by Ian Hau and Ford Calhoun is a good example of lean thinking, eliminating waste... in an innovation setting.
In, Turning Limitations into Innovation, Marissa Ann Mayer explains one of the systems improvements well:
In cases like these, the people working on it have spent so much time and are so personally invested that it's too painful to walk away. They often know the project is misguided, yet they see the effort through to the painful, unsuccessful end. That's why it's important to discover failure fast and abandon it quickly. A limited investment makes it easier to walk away and move on to something else that has a better chance of success.
This is a great example of applying management improvement ideas to innovation. You need to look at the system of innovation. Determine weaknesses in the system. Implement procedures to counteract those weakness. You also want to systemically support what is good, of course.
The PDSA cycle is a great tool for innovation, even for only for a portion of the innovation process. Other "lean" methods that support innovation: long term thinking, respect for people, constancy of purpose (shared vision), customer focus).
The tools (of quality, TQM, six sigma, lean thinking...) each have benefit. Those tools can be misapplied in relation to innovation. That would be an example of using the tools improperly, not an example that lean (or six sigma) doesn't work with innovation.
Yes, Deming knew you need to manage what can't be quantified and I believe lean thinkers do too (six sigma proponents might have more trouble with this but they can see this too).
DeBono, Hamel and Christensen have many good ideas on innovating effectively.