In short, and as you said yourself, we are not privy to what Mueller is looking for ultimately & how strong or weak their case is at the moment. With regards to Flynn, considering how grave some of the stuff alleged in the press has been (including selling to Turkey the service of extraditing somehow a prominent opposition figure from the US), the charges brought out so far are pretty tame.
Which I think that is why it is sending strong signals to people more versed and privy to the way these investigations work. And More narrowly how Mueller operates. At least from what I have gathered trying to figure this all out.
Because the charges brought on Flynn are incredibly mismatched with what most reasonable observers think Flynn is exposed to. That such a mismatch would not exist if Mueller was not expecting some major substantive cooperation at exposing at least someone higher up the food chain, whoever that is. But there are only a handful of people that could be.
The second inference I keep reading and listening to prosecutors familiar with these types of investigations is Mueller is engaging in a type of signaling, which I first heard mentioned during the Manafort arrest: look at Flynn and Papadopoulos, if you cooperate with us this can be you, if not, look at Gates and Manafort. The train is leaving, tickets are limited, you would be wise to get the few ones remaining or its come what may be for you. And we will
not be gentle if you don't cooperate with us.
Which is all substantiated further by Mueller's prosecutorial history. Where he gave, by any account, an incredibly lenient deal to Sammy Gravano and his laundry list of murders(I think released this year on a light 15 year sentence) in exchange for his enormously substantive deal that turned him into the star witness that brought down the Gotti crime family.
Beyond those two things I think it is hard to infer much else at this point. Except to maybe say it would be a legacy crushing blunder if Mueller doesn't feel confident he can end up catching someone further up the food chain on substantive charges or exposure and he merely lets someone like Flynn skirt on such paltry charges for a failed move on Kushner, McFarland, or Trump himself.
