Kelly's Xs and Os will win in any league. He plays the numbers game---it's really quite simple. If you zone him he overloads it, just as any basketball team would do. If you go man on him, he will try to exploit what he considers to be his best matchups.
What Kelly does so effectively is he stretches the defense out vertically AND horizontally. He makes you cover the entire field, which as we all know is quite a challenge for any defense.
Where Kelly is getting in trouble in the NFL is with his up-tempo. In college you have the luxury of having well over 60 players on the roster. In the NFL, he only gets 45 and thus he is getting his players gassed and frequently running them back out there too soon. As an NFL head coach, you don't want your defensive players disgruntled and overwhelmed. It's one of the reasons why coaches try to run the ball as much as they. They need to give their defenses some much needed rest in between series.
I think that if Kelly dials the tempo back, he will succeed in the long run.