I see your point with Pele, but he did step up in the big stage (world cup). I would say that him and Messi are perhaps on a par atm, because of Messi's amazing club record. But to over-take Pele, Messi needs to step up in an international tournament imo.
So the Champions League isn't a big stage then? 4 Golden Boots in a row, already comfortably the leading scorer in the knockout stages ever at the age of 24, will probably come close to doubling the all time scorers record by the time he's done. 73 goals this season, Pele couldn't even manage that in the shitty Brazilian League, but he played well at a few sub 10 game tournaments in some of the best teams ever that probably would've won without him, so that automatically makes him a better player. I'm not trying to degrade the World Cup, but international football is the minority of a players career and should supplement a players domestic achievements and performances (see Cruyff, Platini, Maradona).
Messi is already above Pele and he's 24. One bad World Cup in a team that called up over 70 different players that year, couldn't defend and were lead by a crackpot manager, but it's no biggie, he'll come big in the next one
By the way, Pele knows all of this, which is why he's constantly telling Neymar he doesn't need to move to Europe and making himself a laughing stock by hailing him as the best player in the world.