So there are two different things here that you are conflating: the specific pardoning of Michael Flynn and whether lying to a federal agent should be a crime.

So there are two different things here that you are conflating: the specific pardoning of Michael Flynn and whether lying to a federal agent should be a crime. Lying to a federal agent is a crime because the Government wants to make it easy to investigate crimes. Hence, lying to them being a crime. You are wasting the taxpayers money by mis-directing the investigators who represent us and are supposed to be investigating crime. That seems reasonable to me, though I did spend some time working as a contractor for the FBI, so I might have incorporated their views too much. Michael Flynn's case in particular was a travesty because of the pardon power, a weird old legacy of monarchy brought over into our system by people who didn't really think it through, like a lot of weird, arcane corners of the US government. Pardons in general I think we would be better off without. Either it is used for small-bore corruption of the justice system like this, or it is used for things that really ought to be moved through the traditional justice system (pardoning all of the Vietnam draft dodgers, pardoning Nixon, etc.).