Naruto himself wins.
He can spam nuke-level attacks, send out clones that can make nuke-level attacks, and defend against nuke level attacks.
If nuke-level attacks are banned, well, he still sends out super-powerful unstoppable clones.
I mean, even if we were just talking lesser stuff, there's a major problem with shapeshifting assassins killing our leadership, even relatively minor ninja are a threat, but the big hitters are simply beyond us. Anything we have strong enough to hurt even a special jonin level ninja is unlikely to hit one, and the true big hitters can defend against our biggest stuff.
What's to be done about Aburame? They get near a battalion, they stay in hiding, and bugs kill everyone.
A Yamanaka? They possess soldiers, walk right past security, and kill leadership and blow stuff up. Or captures leadership and mind-reads them.
Mass genjutsu? Everyone in a base just falls asleep. People in planes fall asleep and crash. There's nothing we can do about it.
Earth jutsu? Slip underground, go to an airfield, destroy every plane on the ground.
All by people nigh invisible from the air, who are fast enough that missiles stand little chance of precisely targeting them, and who can also work together to put up regenerating barriers that can stop our strongest bombs.
We're not designed to take on ninja.