Waterfall project management works really well as long as both the solution and the problem are already well defined. Since this is so rare in innovative organisations, you might look to agile methodology for answers on how to plan in unknown changes to your project plan.
Agile project management is designed for situations where the problem is well defined but the solution is unknown, so by building iteratively you can increase the likelihood that the project is a success.
Lean principles are applied to the full customer lifecycle and are focused on creating as much value as possible to the end user by validating learning and gathering feedback as frequently as possible. Lean principles work really well in combination with agile development sprints.