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Several things are coming together here for Real Madrid: first of all you got the Mbappe transfer and as has been said here in the thread countless of times, everyone thought that this transfer will make a huge difference for Real Madrid and lift their game onto the next level, but so far that has not happened. Secondly, Real Madrid has to cope with so many injuries and at some point, admittedly no coach in the world would still be able to build the perfect squad. They have lost two of their most important attackers, Mbappe out of shape and some other injuries in other positions, like Alaba still missing for example. Thirdly, their midfield is not the same anymore without Kroos and Modric who is getting older and older. This makes a big difference for them as these guys have been playing and working like a clockwork. I doubt that they will be able to soon replace their midfield with players that are of the same quality as Kross and Modric in their prime.
I agree with the three things you said. Adaptation, player transition and injuries are three things that Ancelotti is dealing with at the same time. Maybe if Real Madrid current manager was not Ancelotti, we would all see them in the middle of the standings, and probably would not qualify for the last 16 of the Champions League. Luckily Real Madrid have a manager of Ancelotti caliber. The ideal squad built by Florentino Perez for Ancelotti has not worked optimally, maybe it will take longer to see Real Madrid perform at their best.