Those apologetics certainly took a lot of contorting there.
First off, it's already been made clear dozens of times that non-criminal yet still critical investigations occur.
Second, you are ignoring the fact the NSA has transcripts of Flynn's discussions with the Russian ambassador and that is what led to the obvious, his conversations with the ambassador were incriminating.
Then what was this supposed to insinuate outside of the reason he gave?
Flynn did not resign to 'spend more time with the family'.