I think they are both exceptional players in their own way. Ronaldo is an amazing goal scorer and an incredible athlete. He trains like nobody else and shows that on the pitch. I see him like an improved Gerd Müller.
Messi is overall a better football player (by far). Messi has an extraterrestrial dribble, an amazing vision and an inch-perfect pass. Next to that he also scores a lot of goals. Messi is widely compared to Maradona, Pelé and Cruijff and in my opinion he surpassed all of them.
Based on last (La Liga) season, the only aspect where Ronaldo surpassed Messi was heading. All the other important attacking qualities were in favor of Messi. Check out this video for an overview: 
RE: Who is the better football player