Flynn also pleaded guilty to lying to the FBI about his work for Turkey. This is on top of his lies to them about contacts with Russia and him actually being fired for lying to Trump/Pence about said contacts with Russia.
Again, I'm no prosecutor, but the last thing I'd do is put my star witness on blast as a compulsive liar who can't be trusted, charge him with and allow him to plead guilty to perjury, then rely on his testimony and/or expect a courtroom to lend any credibility to his testimony. A competent defense attorney would have a field day during cross examination.
In my non-prosecutorial opinion, if Flynn truly had the goods on Trump, there's no way Mueller shits on Flynn's credibility like he has and charges/allows him to plead guilty to perjury before his courtroom testimony.