Hmmm, I think Frog. Disregarding their game stats, I think he has a few advantages:
1. Frog is a trained knight, trained from a young age, it seems, and regarded as one of the greatest swordsmen in history. He's the 'Legendary Hero' and the only one who can wield the legendary 'Masamune', which he can use to split a cliff in half! Crono on the other hand, is a young man who still lives with his mum, and who, it seems has had no formal training. Though he's a naturally talented swordsman, I think Frog's experience would give the amphibian the upper hand.
2. Katanas are really great for cutting through flesh, but the truth is that (despite many myths) they are not very good at all against armoured targets due to the fact that the sharp blade notches easily and doesn't have the weight needed to bash through armour. trying to parry Frog's broadsword would also probably break Crono's katana, and so Frog has the upper hand in defence too.
3. Frog is extremely agile, and also small and wierdly shaped. Iaido (training with the katana) focuses on how to fight against a human oponent, not a humanoid frog! Frog then has the advantage over Crono because he knows the limitations and weak points of a human body better than Crono will know his own physiology!