It's fairly obvious what is the main reason for that. Ronaldo has a clear position, and a specialized role. Messi does not. Messi is the offensive game of Barcelona, by the way he is used, and the way he moves. He goes everywhere he wants, left, right, center, moves where he wants, when he wants and everyone has to adjust. If he drops back everyone gives him the ball. If he walks and doesn't cover an area, someone else has to pull a double shift. He has complete freedom, and for the system to allow that to a player, it means other areas have to suffer. Areas that suffer are very important: defensive transition in the first few seconds after a ball is lost is almost non-existent. Pressing? Good joke. Covering ground and maintaining shape is also terrible. Messi does almost no defensive work whatsoever. Doesn't even bother to press or close a pass that is 10m. away from him almost.
Ronaldo doesn't do that. That's not the way he is used. You won't see Ronaldo drop 40m. so he can take the ball from Kroos. But you do see Messi wandering around in midfield and vacating his position whenever he feels like.
So you have a specific part of the working system that is failing (Ronaldo), vs the system itself that is failing because it is designed to enhance a player that is not decisive enough on the night.