If his fitness is that bad then he needs to come off and allow himself to get properly fit again.
It is clear he doesnt like missing games or being substituted and it is something that needs addressed.
I'll reply to the other posts later, but in regards to this one, I semi-agree. If it is a problem then it does need to be solved.
However this is a very unique case we're dealing with so it's not easy. This is the biggest legend in the club by far and the best player. He's played an astronomical number of games every season for most of recent memory and tends to deliver when doing so. Do you think it'd be logical for him to doubt himself or ask to be played less? It's something he'll have to come to terms with more as he ages and it's not easy because the decision is pretty much entirely in his hands. Most other players would get rested/benched after poor performances due to competition with other players. Messi hasn't been affected by this since he was a teenager and he's still by far and away the best option in his position, competition will never threaten him until he's truly declined. It might not be totally fair but it's reality.
It's not the go-to call in a 29 year old player's mind to stifle himself. It's also not easy to tell a player who has been performing at a ridiculous level for practically a decade that concessions will have to be made with regards to certain matches. There were always going to be a set of issues that come with having a player with such a ridiculous level of talent AND longevity, I actually kind of feel grateful to have this problem now that I think about it
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This current coaching staff and the next one need to figure out a way to make it work though. Off the pitch, he needs (and probably/hopefully already gets) a high level of individual attention to his regimen to keep him sharp and fit in training. The nutritionist was a very good call and similar ones need to be made. It's a necessity to rest or sub him more often in dead rubber matches. You could also fine tune the circumstances of Messi's walking that he expends less energy in small matches and is sharp for bigger ones. I don't know if Messi has ever had this conversation with the staff so we can't really know how much of his walking at the moment is done by design. If they haven't discussed it, then they need to. Every aspect of Messi's decline needs to be explicitly handled so as to mitigate the problems and keep him fresh/healthy when we need him for as long as possible. The best player in the world requires the best handling and care in the world, it's the only logical way to extend the lifespan of Messi's prime.