The FBI has been after this guy for years. I think in this case Mueller saw this fake investigation as an opportunity to settle some old scores.
Read the guy's biographical profile. If you just read his background and didn't know who he was, you'd assume he was the person Donald Trump had in mind when he described "The Swamp" in Washington, D.C.
Manafort made a fortune selling influence in D.C. to foreign interests. I've long ago conceded that there's a strong possibility he was as crooked as the criminal charges against him make him out to be.