Flynn would have to be awfully patient and trusting to bank on pardons and exoneration in the snake pit that is Washington. An alternative is that Mueller has something on Flynn and/or his son that has nothing to do with lying about conversations with Russians during the transition, and sufficiently dire that he’d rather take the plea deal and shut up than contest it and find himself charged with other offenses. In this scenario, the US does not desire a public airing of the “something”.
Based on this, I will be pleasantly surprised if Flynn’s defense does anything with Mueller’s data. The judge might have some legal way to vacate the plea deal/conviction if he finds malfeasance by Mueller’s team. I wonder if Congressional committees could provide evidence to the judge for “comparison purposes”.
Oh, the judge most definitely CAN intervene if he judges that the Mueller team has acted inappropriately, withheld exculpatory evidence, etc. Whether the judge WILL act is a separate question, but there is no doubt that he has the prerogative to act.
I'm not a lawyer, but I believe the protocol in this case would be for Mueller to charge Flynn with everything he has on him, and then agree to drop all the other charges in exchange for the guilty plea. A number of people who have analyzed these cases in the media (Andrew McCarthy, for one) have explained how this whole approach by Mueller is highly irregular for this particular reason.
And in any case, there may also be an issue with bringing future charges based on the legal principle known as the "Entire Controversy Doctrine." Under this common law standard, any and all claims against a party must be brought at the same time, or they cannot be brought later. There are some exceptions to this, but I believe Mueller would not be able to bring charges against Flynn later that he didn't bring already.