The argument that he did it in more leagues is not valid at all. It doesn't mean much. Prime Messi tears up any league, and it wouldn't be pretty for his opponents. The problem with Messi is his attitude and mentality. Ronaldo simply beats him clearly in this area.
I have it quite clear personally. Overall, a tie between Ronaldo and Messi with each having its own advantages over the other.
Messi has:
- brighter peak of Maradonian level
- more talent, IQ, creativity (so-called X-factor)
- a more complete style (equally great at passing, playmaking, scoring, dribbling)
- better dribbling (which is arguably the most spectacular aspect of football - the ability to ridicule players with the ball)
- more consistent in the league
Weak points, especially visible in the 2nd part of his career, post-peak
- lacks leadership
- subpar effort and often poor attitude in high-pressure situations
- poor scoring form in the Champions League in big games (especially away)
- quite undisciplined and hard to manage (can't be a role player and needs the team to function around him)
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Ronaldo has:
- better work ethic, professionalism, and dedication
- better athlete (just look at his fitness level at 35)
- better finishing skills (shoots with both feet, great box-predator, near unbeatable in the air)
- better clutch performances which he also carried past his prime (hence his superiority in CL)
- slightly better career
Weak points
- not as bright peak
- dominated by prime Messi (also in h2h)
- not as a complete player, more of a specialized role
- not as many brilliant moments
As you can see, plenty of flaws and plenty of areas where they dominate each other. It's unlikely anything will change at this point in their career.