Messi is a better passer. Ronaldo is a better finisher whether it's shooting, heading, free kicks, etc. Dribbling is very close as they are both extremely technical dribblers, but they have distinctively different styles. Messi chooses to be much simpler which benefits his passing game as he looks to just use simple cuts to go pass defenders. Ronaldo has just about every trick in the book as far as dribbling goes, but he is most effective when he is direct and uses his pace. Ronaldo clearly is better physically as he is bigger, stronger, and probably a little bit faster.
Really, comparing the two to see who is better is silly. They are two amazing, but different players. I do think Messi is in the perfect atmosphere for his style of play. Ronaldo has proven effective in more than one system. The fact is it's really too tough to tell whether one is better than the other. Messi will get the popular vote currently, but that's just a popularity contest.