Most organizations have mastered the ability to deliver their products and services reliably and efficiently. Remember the 99% lists? As consumers we've come to expect excellence, and companies that don't deliver above and beyond this excellence won't last very long.
Organizations themselves also take these skills for granted. I'm often reminded of this when I'm working with clients to develop innovation processes. Many of the people within companies become frustrated that the organization's capacity for change is so low.
At this point, it's helpful to step back and really think about what your development and manufacturing processes are expected to do. If you work in a business where 99.9% isn't good enough (most organizations), then expecting the current process to accomodate breakthrough innovation is just not realistic. Alternatively, expecting that the outcome of the innovation process will be products and services that fit neatly into existing systems is equally unrealistic. Innovation efforts that implicitly carry either of these expectations will most certainly fail.
Innovation processes require room for experimentation, trial and error, incorporating unpredictable human elements, and all the other things that would bring current development and manufacturing processes to a screeching halt. It's far better to separate each process, and let each one be what it needs to be. Your innovation process should result in the identification of new opportunities that can be delivered in multiple ways. Some may be able to work with slight modifications to existing processes. Others may require completely new processes.
Your innovation process should deliver market relevant opportunities. Your development and manufacturing processes should deliver offerings to the market reliably and efficiently. The real organizational challenge is managing expectations within the organization for what each process should deliver, and establishing the right connections between them (more on how to do that later). But don't expect one to deliver on the expectations of the other.