If both of them use their plane to fight, fox will flawlessly win. Why? Cuz fox has robotic feets to help the circulation of the blood when he is in the air. So he will have no problem, no pressure to take aim to take out his opponent.
I think you are right about Fox being a more experience pilot, but robotic feet suggest that Fox's Arwing aren't advance enough compared to Ratchet's Ship. Ratchet never chopped this own legs to become a faster pilot. Fox so far came to three solar system and Ratchet came to three different galaxies; Fox needed the Beltino Orbital Gate to get to the Aparoid Homeworld. Ratchet's ship the Aphelion is different from the Arwing; it has rear-facing turret which can be opperated by Clank. Meaning that attacking Ratchet in the back might be difficult.