Here is a the Hill article that addresses two questions that are puzzling :
- Why did Flynn lie to the FBI, and
- Why did Mueller charge Flynn with lying.
http://thehill.com/opinion/white-house/362948-why-did-flynn-lie-and-why-did-mueller-charge-him-with-lyingOn the first question, they don't get much further than we did here, with the Logan act, and that that is not a good reason for Flynn to lie to the FBI.
So we still don't know, and the plausible reason is that there is/was a much bigger conspiracy going on between Russia and the Trump campaign. Or some sort of unwritten rule within the Trump campaign and transition team that you should deny everything that has to do with Russia.
On the second question, the Hill notes correctly that if you want a witness to testify for you, that you should not charge them with lying. After all, if they lied once, they can lie again, and thus you can't use them as 'credible' in a trial. The Hill concludes that this exposes a weakness in the Mueller strategy that they didn't charge him with something like "conspiracy", and they suggest that Mueller doesn't have enough evidence. The Hill does not explain what a charge against "conspiracy" would actually look like in legal terms.
So I don't think it is a weakness. I think that Mueller is not going to rely on 'witness' statements that much any way at this stage in the investigation. And especially not with Flynn, who resigned because he lied to the VP. Mueller is just using hard evidence at this point. Emails, recorded phone conversations, documents, wiretaps etc. Flynn was under FBI investigation for a long time, so they probably taped every one of his phone calls. That's how he got Flynn to admit that his conversation with the Russian ambassador was about sanctions any way. The FBI doesn't kid around.
Mueller will take this one small step at a time. I think it will take a while until he uncovers the truth and the whole truth of what happened during and after the Trump campaign and their relationship with Russia.