First, innovation is not limited to what is of interest to a CS PhD program.

Second, I'm not interested in "innovating" per se, I'm interesting in creating things that add value to peoples lives and not being pigeonholed as either an engineer or a product person. I don't care if the ideas I'm using are new or not, only if what I'm building is enriching someones life and that my product has users.

Third, I've never been a replaceable number at a company, even large companies. If you work on hard problems, and are good at it, you aren't easily replaceable. People realize this, even when you're working for the man.

Finally, at university you often don't have access to real world data to do research. I know some big universities like epfl do partnerships where they work with researchers and engineers at companies in exchange for access to that companies data for research and publication.

However, there are just as many counter examples. Elon Musk left Stanford's grad school after one day!