It's not just goals scored though, is it?
It's how you score them and what else you bring to the team.
I'm not saying this as a direct comparison between Messi and Pele as I've never seen Pele play, but Messi scores unbelievable individual goals, and when he's not scoring he's usually assisting. Take for example the 53 goals scored by Messi and Ronaldo last season. Now look at how many penalties & tap-ins Ronaldo got compared to Messi. Whilst it can be argued that you still have to score the penalty, and still be in the right position to score tap-ins, it is a considerably easier goal to add to your statistic. I am terrible at football, but give me 11 penalties in any league or competition and I'm sure I'd score some of them, and there you go, I've got goal/game statistics.
Statistics are not enough alone to judge a player. It's the quality of Messi's goals, and the amount of assists and influence he brings to the team that give people reason to call him the best ever, not just the fact he scores a lot.