Maradona and Pele played against far more physical opposition than Messi did. But that's it really. I still don't buy into the fact that they were on the same level as some of the modern players. Yes, they had to deal with defenders chopping them down, but the game has evolved for the better now. Even with the restrictions placed on defenders, those at the top of the game - your Kompanys, Vidics and Kings, still manage to win the ball off opposition players regularly and almost never get skinned by a tricky attacking player. That shows that the standard of defending is far far higher than it was in the 60s, 70s and 80s. You also need to look at the levels of fitness across the game now. In the 60s, 70s and 80s, there were big drinking and smoking cultures amongst top clubs in the game. Now? Most top players are completely tee-total. They have carefully designed diets. Has anyone recently watched a full length game from the 60s? By the end of the game the players are so tired they're practically playing at walking pace. Messi on the other hand is constantly on the move and always still has a burst of pace left in him in the 90th minute to win the game.
Another big advantage that Maradona and Pele had over Messi is that, while opposition players would have known about them through reputation or seeing them in action once or twice, they never had the opposition watching DVDs, studying their style of play, their movements, their strengths, weaknesses, analysing every little detail of their game to work out how to stop them. Everyone knows what Messi can do, they just can't stop him from doing it.
Since the big money came into football in the 90s, clubs, coaches and players have been forced to become more and more innovative in their approach. Standards of football have never been higher in terms of the average quality of players. Blackburn won the league in 1995 with Tim Sherwood as their captain and players like Jason Wilcox and Stuart Ripley as important first team stars. Players of that standard wouldn't get anywhere near a top side these days. Nor would Kenny Dalglish be able to manage a team to the title. Standards at the top level are way way beyond what they used to be, so to excel at the top level is a greater achievement than it's ever been.
Perhaps if you brought Pele and Maradona into the modern era they'd still be stars. But it's not fair to compare them to Messi because they're not proven at the same level. It would be like comparing Kris Boyd to Sergio Aguero because Boyd has won the SPL golden boot a few times and has scored a few goals in the MLS whereas Aguero has never won anything. The players who have been at the top over the last 10-15 years are the best of all time because they're the ones proven at the highest level.
For me, the best player of all time is either Messi or Zidane. I'm leaning towards Messi.