Number one reason why I believe the players from early 2000's, late 90's (what I've seen) are much better than today's players is because of defense. The art of defending is almost a lost art nowadays, teams need to defend in large numbers (park the bus as they call it). Freaking Nesta at 37 DESTROYED the BEST player in the World and arguably one of the best of all times. Now imagine the likes of Messi\CR7, etc being up against defenders like Nesta, Canna, Thuram, etc.
Even Chiellini, Thiago Silva, Vidic, etc look bland and average compared to the great defenders from the past. Speed and athleticism are important factors but that's not what made Pirlo, Nesta or Del Piero some of the best players of all times.
IMO there's a direct correlation between the level of defending and the talents around, great defenders force strikers\players to be even greater. Until we see more of the likes of the older defenders I think the likes of CR7, Messi should never be uttered in the same breath as DP, Totti, Raul, etc.