I'd say that overall it's a decent list even though there are obviously a few positions that I disagree with. The thoughts below were usually based on the comparison between the players with similar roles to avoid confusion.
Overrated:
Zidane ahead of Di Stéfano, Cruyff, Beckenbauer, Puskás and Luis Ronaldo is laughable. I'm also of the opinion that he's not the best ever French player, Platini is, but that is at least debatable.
Carlos Alberto at 25 when Cafu is at 76, Alves is at 73, Lahm at 85 and Zanetti is at 96 seems like an odd inclusion. It's not even a given that he was the best right back out of the 5, let alone being 50+ places ahead of them.
Paolo Rossi at 42 ahead of Henry, Law, Greaves & Kocsis is a bit of a joke. A very good player but clearly a level below the very best — and I'd put him below the likes of Benzema, Lewandowski and Suarez who didn't even make the list. That Ballon d'Or confuses the hell out of people. Even at his peak he was probably the 4th-5th best player for his club behind Platini, Scirea & Boniek.
Johan Neeskens at 65 with Rijkaard at 77 (the most complete midfielder of all-time alongside Matthäus), Modrić at 79 and without even the mention of Keane or Redondo is an oddity.
Jairzinho (53) is a tad too high compared to the likes of Rummenigge (61), Stoichkov (89) & Kempes (99)
Underrated:
Rijkaard, Modrić, Figo
Notable omissions:
Figueroa (best ever South American defender), Nesta, Thuram, Krol, Breinter, Bozsik (weird, considering the inclusion of Hidegkuti, for example), Keane, Redondo, Rivaldo, Dzajic, Czibor
+ a bunch of strikers like Shevchenko, Benzema, Lewandowski, Suarez
More debatable corrections:
Best probably deserves to be up there on pure ability but, again, when you compare him with similar or almost similar-talented players in Ronaldo, Puskás, Di Stéfano etc., you have to give a nod to their longevity.
Pelé, Messi & Maradona is a settled top-3 for me personally but it's not like inclusion of Cristiano is criminal — it's just something that I personally disagree with.
Also probably should be changed: Xavi > Iniesta (even though I love the latter more), Baresi > Maldini