Kroos actually even played occasionally as a single DM during Madrid's La Decima season, before Casemiro was integrated into the team. He's certainly no Kanté but he's relatively good at intercepting and anticipating, a bit like Busquets. Gündogan has also played the Fernandinho role for City under Guardiola. I think you're exaggerating a fair bit.
Especially since we would be very flexible with Kimmich as an "inverted RB". In possession you'd have a midfield consisting of Kimmich, Kroos and Gündogan or Goretzka, depending on who of them goes forward. On the right wing, Gnabry provides depth and on the left wing it's Gosens, e. g. This would also work well with Werner as a LW who makes many runs into the center and naturally leaves his side exposed now and then. Havertz as a false 9 would also work well with either Gündogan or Goretzka pushing up and Werner making runs inbehind. And with Rüdiger and Süle we even have two fast CBs in the team again to provide the pace Hummels is lacking.
Madrid's La Decima season was in 2013-14, when Kroos was still at Bayern. In the three titles they won following, from 2016 to 2018, Kroos was with Madrid but Casemiro was firmly in the side by then as part of that famour Madrid 3 midfield.
Gundogan was playing the Fernandinho role last season mostly and was criticized by City fans for those performances, though they were mostly when playing alongside Rodri, who himself was getting used to playing in England. The argument was that Gundogan and Rodri were too slow and passive to be the defensive midfielders. Playing as a DM has arguably been Gundogan's weakest performances for City, even previous to this season his best season was the 2018-19 season when De Bruyne was injured for much of the season and Gundgogan played alongside Silva and Fernandinho.
My favoured line-up would be:
---------------------------Neuer---------------------------------
-------------Sule----Hummels---Rudiger----------------
Klostermann-------------------------------------Halstenberg
------------Kimmich---Goretzka----Gundogan------
--------------------Gnabry----Muller-----------------------
I prefer the 3 man midfield because I don't trust Rudiger as part of a 2 man central defense. Rudiger has been in amazing form and therefore I feel should be in the team, but that has been as part of a 3 man midfield, playing in a 2 man midfield is entirely different. It will also give Hummels more protection and allow him to go forward as part of the buildup without worrying about not having protection.
I liked how Germany generally played with the 3-5-2 midfield when Low tried it with Gnabry and Sane as the front two. Muller has to be play given his immense form. Kimmich would seem to make more sense as a RB given our weaknesses in that position, but he's our best midfielder and therefore should play there to maximize his ability. I'm also not as negative about Klostermann as others.
If we have to play 4-2-3-1 then I would drop Rudiger and play Sule-Hummels, drop Gundogan and bring in Sane as a LW (Gnabry RW) and Muller is the CAM.