By cutting out the red tape and bureaucracy that frequently make people think "big == bad". Company size is just a proxy for other factors that can lead to a negative work experience. What I care about is not the size of the company but how much impact that company is going to have on me trying to do my job. HR policies that prohibit being paid what I'm worth are an obvious example of this. Multiple layers of management who need to sign off on my work or second guess my judgement are another.
None of these are exclusive to large companies, and while small companies tend to be more flexible, that doesn't mean that they are categorically better places to work.
Look at Lockheed Martin's SkunkWorks, for a great example of a large company setting things up to attract and keep the best engineers in their field.
Funny you should mention SkunkWorks - that's actually the one thing I was able to communicate to him was the SkunkWorks concept within a larger company. But clearly if everyone is working that way, then it no longer has the delineation from regular business that is the whole point of SW.