This is a tough one, but I believe Sonic would win the battle. Why?

Well a few key points, some of you have stated that sonic cannot attack while running, and I find this to be not true at all. While sonic was running circles around Zero, he could begin roll to smash into him, and then bounce while rolling before he hits Zero to go for a critical hit. Now, why wouldn't Zero just slash him to death? All of Zero's attacks have a slight weakness in them. After using one of his saber specials, theres a half second or so where his saber is still retracting. That is when Sonic could strike him. He should have practice at this sort of thing, that slight half second opening is the key to defeating many of Robotnik's creations! If Sonic had access to the fireball special, then in all certainty I think the fight would be over. Not only does the fireball powerup block any projectile attacks Zero could fire from his arm cannon, but Sonic could instantly launch himself at Zero, as a burning ball of fire. The most Zero could do is dash to block. Sonic would have a large advantage in both speed and damage. Even if Zero could 'see' all of his moves, it does him no good unless his chassis can respond fast enough.

And I won't even go into the area of Super Sonic or Hyper Sonic.. heh.