There has been a lot of speculation about Flynn's bargain with the Special Counsel. This article provides a good framework for understanding Flynn's deal and how it might be used by Mueller. Its pretty clear that Mueller would not have made the deal with Flynn unless he was given something in return from Flynn that would be pertinent to his investigation. We don't know what Flynn can tell us about those above him in the White House. But we do know that he did not operate as a lone wolf. We also know that there were not many people who outranked him in the inner circle, and that his position as national security adviser gave him access to data and discussions that are only available at his level. Trump did not go out of his way to terminate the FBI investigation of Flynn because he likes Flynn. What just happened is just what he wanted to avoid. Mueller will now interview Trump's inner circle and they will have to be careful in their answers to his questions because they are aware of information that Flynn may have provided to Mueller.
This editorial in the NYT takes an even stronger position on Flynn's cooperation with the Mueller investigation. Obstruction of justice charge has been strengthened and Flynn may even testify that Trump was involved in his illegal discussions with Russian officials.