I dont think anyone is saying he shouldnt be up there, but his stats, like Ronaldo are a product of the modern game so its difficult to compare his achievements to players of years gone by when the game is totally different no to say when Maradona or Pele was playing. Modern players dont get constantly brutally assaulted like Pele did say in 1966 against Bulgaria and Portugal, or Maradona when he got his leg broken by Goikoetxea. The modern game lets players express themselves without the fear of just being kicked out of games. I think the modern game is much better to watch, but it does allow attacking players to play without fear. I still dont think i would put Messi as the GOAT, but he's probably the best player of his generation.
And as i keep saying, simply using attacking metrics to measure a players greatness is a terribly flawed system of picking the best player of all time when you can have players of equal ability in other positions that get overlooked, which is why the Ballon d'Or isnt a great way to judge the best player in the world in a particular season. I've used him a fair bit, but the year AC Milan won the Champions League and Serie A, he was the best player in the game and the leader of a defence that won the Champions league conceding only 2 goals and just 15 in Serie A, yet he was miles behind the winner of the Ballon d'Or that year. Its an award thats supposed to reward the best performing player, not the most entertaining or attacking player, and i dont think it does.