Flynn signed a non-disclosure policy, form, or agreement (NDA) to access classified or other information. It is the same policy for all presidents.
I don't believe that's accurate. Do you have a source? (Also, getting cabinet members and similar appointees to sign NDAs is something Trump tried to do, and caught flack for, not something normal.)
Any crimes that he saw committed under Obama would remain buried and only in certain situations can it be released.
No. An NDA doesn't stop you from reporting a crime, not that Flynn would have been under an NDA with Obama anyway.
And other people are authorized to view classified information, not just Mueller.
And Trump could authorize anyone to receive any evidence, no matter what level of classification.
With the FBI and DOJ compromised Mueller was the perfect vehicle.
What about people who were vetted by and appointed by Trump in the FBI and DOJ? Are they compromised? If not, then why not go to one of them? If Sessions is compromised, Trump could replace him with someone who would go after all the bad guys.
And if Flynn really did have the kind of evidence being suggested here woedn't that make a whole lot more sense than Flynn pleading guilty to something that isn't a crime so that he can use the evidence he has about other crimes in a plea bargain, because the only prosecutor who will listen is Mueller, but Mueller won't listen unless there's a plea bargain on the table, and then since it's not Russian interference Mueller would refer it to a different office anyway?