Really doubt people were comparing Neymar to Messi in earnest, and even if they were, the Campeonato Brasileiro was much stronger in the 40s, 50s, 60s, 70s, 80s in contrast with now. These days almost every good Brazilian talent leaves for Europe once he develops to a certain level and the league has been stripped down in terms of quality. If you look at the current national team, almost all of the starters are playing outside of Brazil. Before the trend began (late 80s-early 90s), they had the likes of Friedenreich, Gilmar, Guia, Ademir, Carlos Alberto, Djalma, Nilton, Falao, Pereira, Jairzinho, Garrincha, Jorginho, Gerson, Vava, Bellini, Zagallo, Zico, Tostao, Socrates, Mauro, Rivellino etc playing in Brazil for the bulk of their careers. A lot them coincided with Pele's time in Santos.
The difference between the current standards (or when Neymar was there) in European football vs Campeonato Brasileiro is massive, no doubt about it. But as mentioned before, the league was a different beast in Pele's time and there were a lot of top quality Brazilian internationals who chose to stay in their homeland instead of signing for European clubs, thus elevating the quality of competition in the league. These days even average players join CSKA, Spartak, Sporting Club and further bring down the median level. Also if we're holding comfort at Santos against Pele, why not bring up a similar argument for say Messi (I love him mind, not to diminish his accomplishments) who has only played in the same system for Barcelona at senior level. And just like Pele has help around him, Messi had Xavi and Iniesta and Puyol and Eto'o at various periods in his career.
The Santos team with Pele was one of the strongest club sides in the history of football and he played the biggest part in their dominance, but because of a lower amount of limelight it doesn't always get recognized as such. eg. Benfica was at the pinnacle of European football, one of the 3 or 4 strongest teams in in the mid 50s to 60s, won 2 European Cups on the trot, and consistently reached the latter stages of the tournament including the final vs United. They had Eusebio, someone who's considered to be one of the Top 10 footballers of all time, apart from the likes of Simoes, Augusto, Aguas, Coluna, Santana. But Santos dismantlement them in the 1962 Intercontinental Championship by a margin of 8-4 with Pele scoring 5 goals in just 2 fixtures home and away.
To put it in perspective, in the 1961 European Cup final - Benfica had beaten a Barcelona team with Kubala (Barcelona's highest competitive goalscorer ever before Messi broke his record), Suarez (one of the greatest playmakers of all time, thrice ranked in the Top 3 Ballon D'Or rankings, and a key component of Herrera's Grande Inter team), Czibor (one of the best wingers of all time and a key component for the Mighty Magyars), Kocsis (Hungary's greatest player behind Puskas). In 1962 they beat Madrid in the final, a team that had won the first five European Cups on the trot and had the likes of Di Stefano, Puskas, Gento, Santamaria, Del Sol. And that Benfica team had no answers for Pele, he could really cut his mustard against the best of them.
Pele was the original king of football and perfectly capable of producing moments of decisive magic from a very young age, starting with the winner vs Wales in the quarterfinals and further 2 in the World Cup finals vs Sweden in 1958. He didn't always run 50 yards with the ball like Diego could, but some of the goals he scored and things he executed with the ball kind of even defied gravity and rules of physics as they're applicable to mere mortals. And while in the interest of fairness, Maradona had a lot of superior natural skills in terms of dribbling, close control ability and so forth, football are judged by a very diverse spectrum of qualities. Pele's uniqueness was arguably his stature as the most complete footballer ever - an improved version of Johan Cruyff or Di Stefano as it were. He could shoot with both feet - long range or in the box with either finesse or overwhelming power, superb header of the ball and dangerous on set pieces, extremely cerebral and anticipated patterns that others didn't, great timing in and around the box, gifted athlete for that era, a very good tackler and played in a collective as a team oriented footballer.
His dominance was supreme - Sao Paulo league top scorer for 11 times, Copa Libertadores top scorer, Copa America top scorer, 92 club hat-tricks, helped Santos to 10 state championships, 5 Brazilian Cups, 2 Intercontinental Cups, 3 World Cups victories with 10 assists and 12 goals in just 14 matches and an overall international record of almost a goal per game - the bigger the stage the better he performed, and kind of changed the way football is officiated - the genesis of yellow and red cards are linked with the roughhousing tactics in 1966. Things fade with time - but he was really a pioneer for his era in terms of his briiliance, and individual or collective accomplishments, and the influence he had on the game are kind of unparalleled. IMO Pele's presence helped and motivated some of his illustrious teammates more than their presence helped him. Best player ever IMO, even though I deeply admire both Maradona and Messi.