Ronaldo is all-time great scorer. He will go down in history as one of the best in that aspect. However, he comes up short in some other aspects of the game. Ronaldo is a WINGER but his passing, vision and distribution are pretty ordinary at best. His style of play is very individualistic. His defensive work as a winger has also been questioned in the past and opposing teams have taken advantage and attacked down his flank although that aspect has definitely improved in recent times. The great players weren't just great players themselves but made others around them great and I don't think Ronaldo does that. When Ronaldo doesn't score, it just seems like he's completely ineffective, that's why he was so criticized againt Barca in the past. It wasn't just that he didn't score, it's that he hardly did anything right. It just seems like in games, particularly in the big games, Ronaldo really needs to score to make his mark otherwise he is just ineffective as the other aspects of his game are just pretty ordinary.
Messi on the other hand, doesn't need to score in order to be effective. Look at his assist to Pedro at the Camp Nou in the Copa Del Rey last season or his assist to Alexis in the 3-1 win at SB last year. Or even his performance in the 5-0 win, Messi was one of the best players in the game even though he didn't get on the score-sheet.
Messi's passing, vision, touch and control in tight spaces is far superior and that's what makes him a better PLAYER even though one can certainly make an argument that Ronaldo is a better goal-scorer (even though he has scored less in the same time as Messi while taking many,many more shots).