Everyone thought Bayern was rebuilding and they came back in one season. You never know. Barca was "done" after 7-0 vs Bayern, then came back in two seasons.
It is how Flick has imported again a functioning pressing and passing system what makes this interesting. He took the established players that learned their "trade" and positional play with van Gaal, Heynckes, Pep into a central axis - gave them a lot trust and responsibility and pushed them into the central axis. M?ller, Kimmich and Alaba are the most vocal on the pitch and especially during the Covid games you really saw how much influence they have to the others. At the beginning - whenever Flick made substitutions too early in a match (or the wrong ones) - it got really shaky. The system lives of the positional play. Class work from the fitness team, too - especially during the Corona weeks. They started to work at home via video conferences every day - with equipment the club delivered to them - two days after the break was announced.
Take Pique as example - or Busquets - they are players that excelled in your old systems - but when that does not get followed anymore and it is more and more just about individualism and too many new players come in that aren't educated in it that breaks and makes them less valuable. Then other qualities might get more important. It is the same with some of Bayern's players.
That about the system. Everything else - the personal qualities Hansi Flick has - are more like that from Jupp Heynckes. He really formed a team out of them.
Edit: About Thiago. During Pep's time he was always hanging behind others when it meant physical performances. But that changed 3 or 4 years ago. Since then he worked with a personal trainer in addition to his work in the club and really benefitted from that. He is no Goretzka as he is not as speedy - and no non-stop-runner with an endurance like a rabbit like Kimmich or M?ller - but his numbers aren't bad either.