This is why comparing characters from different verses is tricky/not practiced, everything you said is highly controversial and can be debated against. It would only lead in circles and loose ends so I'll sum this up.
If you think about it, Nen is equal to chakra, and nature energy is something completely different. Most likely frog kata will damage Gon. In the event that is does not, Naruto and Gon engage in hand-to-hand combat and Gon is dominated. Naruto notices frog kata not affecting Gon, switches to ninjutsu and wipes him clean off the face of the earth.
Rasenshuriken + surprise expansion ends Gon, and there is nothing he can do about it; even if we do agree that Nen=Chakra in this match, and Gon can see it.
Equalization is obviously here. Sorry if I didn't mention this.
You're underestimating Gon's ability here. He won't be taken down in hand to hand combat. Gon took a hard beating from Genthru, and got both his arms blown up first. Gon manages to save both. Gon gets obliterated, and Genthru uses his ability seriously. Gon gave up on one arm, and protected the other one, kicking Genthru in the face. Tell me, did Naruto do anything remotely close to this? Attacking an enemy after getting his limb removed, the other one badly injured, and still successfully land a hit? Don't let me complete what I'm saying here. Gon then took out his binder, secretly taking out a card, came near Genthru who tricked him, literally crushed his throat, and gave Gon a clean hit on the neck, although Gon used Gyo to defend there. Look man, he just got his throat crushed, and still had enough concentration to concentrate Nen on his neck. He immediately counterattacked and threw a gasoline pack at Genthru's face. He then used Jajanken on the ground, destroying it. He then did it once more time to knock Genthru unconscious. He even had still enough power to grab Genthru and go back to Bisky and Killua.
Gon is the one who's going to beat Naruto in hand to hand. You're forgetting about Gon's Hatsu, didn't you? Rasenshuriken didn't remove anyone in the entirety of Naruto. It didn't even do anything to Kakuzu, except permanently paralyzing him. He destroyed the Pain body because of how the body works. It does everything through chakra, and the Rasenshuriken destroyed its chakra points. The body was still there. You're also forgetting that in Naruto, they don't have Ren/Ken/Gyo/Ko techniques which protects the body. At the Heavens Arena, Wing displayed that by just touching a Paper along having your Nen activated, nothing else, it becomes strong enough to cut through a metal can and a wall. Even without touching the wall, he shattered part of it. Using advanced techniques such as Ken will probably defend him against the Rasenshuriken, but no doubt it will hurt him a lot.
Back to Gon's hatsu, Jajanken. Gon isn't that stupid to let Naruto prep his technique unless he's up to something. He won't let Naruto take control of the fight. Gon's Jajanken is at least capable of OHKO'ing Naruto.
I say Gon wins more times than not.