Exactly that. Pep wanted a ball-playing CB who could play in an (exaggerated) high defensive line. Benatia is better in a more classical setup. Pep even preferred to use Kimmich and Alaba in CB instead of employing him (facepalm. Pep's choices for the games against Atlético were a huge source of rage for me).
Furthermore, it seems he never adapted to life at the club (which is fairly rare, since Spaniards, Frenchmen, Brazileans, Dutch, Poles have all came in an fit well).
Overall, I'd say it was Pep that killed his career at Bayern. I think with Carlo he would have been a success. Anyway... No need to linger on the past. Hope he does well for you
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