And this is where he beats Ronaldo as a footballer. Messi is just a pure natural gifted footballer whereas Ronaldo is more an athlete. In other words Messi didn't have to work too hard to hone his skills he just has them. Ronaldo on the other hand has had to put in the graft to reach that level.
I agree with you to a certain extent but isn't half the thing with Messi that he has these talents and then combined them with determination and hard work? I bet there are tons of other Messis out there who had the same talent and who were too lazy or thought too much of themselves. A Swedish skier once said something like "People say I'm lucky and alls I know is that the more I train, the luckier I am". I'd say the same thing here with Messi is that the more he trains, the more talented he becomes.
One could also discuss what Christiano Ronaldo's rank in modern football would've been if Messi hadn't been around at the same time. I'm not gonna have it here on this forum though.