I think you're reading way too much into the Flynn plea bargain. He has a whole bunch of stuff unrelated to Russia or Trump that he potentially could face charges for.
His plea is still one of the most baffling things in this, especially if he was central to any kind of conspiracy. Doubly so if his statement that there were no side-deals isn't just another stupid lie.
It almost makes you wonder if he's been told that a husband and wife cannot be charged for the same crime.
We had this one out before and I probably am even more convinced in my thinking today, but there is very little chance in my mind that Flynn is getting a plea deal that is anything but trading up, and trading up regarding Mueller's primary objective in his investigation. It's just not how Mueller operates from everything I continue to read, or from what I have gleaned, any prosecutor really. In any other investigation like this Flynn would be a big catch, so for him to get off so easy it is hard to imagine he isn't giving something up significant. The only possible other explanation I have heard, but it seems reckless, is that Flynn was a stalking horse for other potential witnesses, a "see if you cooperate we will give you the Flynn deal, if you don't you can get the Manafort treatment," hoping to lure an actual big fish....But then who would you really be targeting?
Also doesn't mean he rolled on Trump per se, honestly probably not(or at least not enough) given how bad they wanted to flip Manafort, but there are a lot of very interesting avenues you could imagine Flynn rolling over and it fingering Trump, also plenty where it is some other person, but there aren't exactly a whole lot of fish in this pond bigger than the former National Security Advisor.