I value the people who would be your potential co-workers and the social impact your work makes over how much stock I'd get or the "20% time" I'm given to work on non-core projects.
Startups do give you the opportunity to have a more hands-on role at the company considering the size of the engineering staff. Naturally (if you're driven and you're confident in your ideas and can work well with people), can make a bigger impact at a smaller company/startup than at some of the more established tech giants. I think experience you gain far outweighs the slim chance your 3000 shares of common stock will amount to anything. You can take that experience with you to a larger tech company.