He would be amongst the best coaches not just in the world but in history if season would only last 2-3 months and he could ran his starters to the ground without worrying about rest and rotations too much. But season is a marathon not a sprint.
My first worrying sign was after one of the first games of the season (don't remember which one) when he said something like "we couldn't press for 90 minutes and that will never happen again".
First you can't press effectively with a 36 year old grandpa as basically your first defender. Pep had Eto'o in his prime years who could ran two marathons in one game, Flick has Lewa on his last legs.
So he compensated for that using Lamine and especially Raphinha as first line of pressure. But ofc that brings consequences too as they will eventually get tired. I think they already are and hopefully there won't be any injuries but wouldn't surprise me to see their level drop in coming months. And Lewa is already looking like Lewa of second halfs of last two seasons (remember he started both of these seasons well too).
And second you can't expect to press full 90 minutes for a whole season. No team can do that and no smart coach would expect that from his players. Especially not in a competitive league when you don't have by far the best team like in Bayernliga. Without horse injections that made Goretzka look like Hulk too, lol. So you can't have press, press, press as your plans A, B, C, D,...
Yes, we probably don't have the perfect players for Flick's system but we all knew that when he took over. But if he's as good as some here believe he should still get the most out of existing squad. And not just for first two months of the season. If he wants to stay beyond this season he'll need to adapt because his plan A won't always work. Even "idiot" Xavi adapted and started to use four midfielders when he saw Busi struggled defensively, played 3 atb in some games etc. I don't care what formation we play but at least show some adaptability.
But Flick seemingly only knows one way to play. When that works we look like a top 5 team in Europe. When it doesn't we are in lower table form. I know every team has their up and downs and hopefully we are past our worst but there are some concerning patterns. And I was already seeing things I didn't like when everyone was elated we were beating likes of Valladolid 7-0. Why did we have to beat a dead horse? 3-0 or 7-0 against relegation fodder doesn't matter in a league that uses head to head and not goal difference as a potential tie-breaker.
Why Lamine and Raphi had to play those early games full 90 minutes? Not only you risk potential injuries but minutes accumulate fast so then they were suddenly tired ahead of a tough away game in Pamplona. As a coach you need to look not just one or two games ahead but in what state your team will be in 3-4 months. Ofc there are some things you can't predict but overusing key players early in the season is never a good sign.