According to Lawfare, Michael Flynn's potential crimes and wrongdoings are numerous.

Reports of Flynn’s bizarre behavior across a wide spectrum of areas began trickling out even before his tenure as national security adviser ended after only 24 days. These behaviors raised a raft of substantial criminal law questions that have been a matter of open speculation and reporting for months. His problems include, among other things, an alleged kidnapping plot, a plan to build nuclear power plants all over the Middle East, alleged violations of the Foreign Agents Registration Act (FARA) involving at least two different countries, and apparent false statements to the FBI.

Because of the sheer amount of crimes Flynn could be accused of, experts believe it makes sense that he would agree to cooperate fully with Mueller in hopes of reducing his jail time. The leniency with which Mueller is agreeing to treat Flynn, however, is shocking to experts.

The surprising thing about the plea agreement and the stipulated facts underlying it is how narrow they are. There’s no whiff of the alleged Fethullah Gulen kidnapping talks. Flynn has escaped FARA and influence-peddling charges. And he has been allowed to plead to a single count of lying to the FBI. The factual stipulation is also narrow. It involves lies to the FBI on two broad matters and lies on Flynn’s belated FARA filings on another issue. If a tenth of the allegations against Flynn are true and provable, he has gotten a very good deal from Mueller.

...It reflects something else too: that Flynn is prepared to give Mueller substantial assistance in his investigation and that Mueller wants the assistance Flynn can provide. We are not going to speculate about what that assistance might be. But prosecutors do not give generous deals in major public integrity cases to big-fish defendants without good reason—and in normal circumstances, the national security adviser to the president is a very big fish for a prosecutor. The good reason in this case necessarily involves the testimony Flynn has proffered to the special counsel’s staff. The information in that proffer is not in any of the documents released Friday, and it may not even be related to the information in those documents. Prosecutors tend to trade up. That is, for Mueller to give Flynn a deal of this sort, the prosecutor must believe he is building a case against a bigger fish still.

Mueller has obviously decided the information Flynn can provide is far more important than punishing him with jail time.