I don't think they had many better choices. After Ancellotti, they wanted someone who knew Bundesliga and Bayern well. They approached Tuchel (Rummenigge choice), who has already agreed with PSG, too late as Hoenes was trying to convince Heynckes to stay for one more season. Hoffenheim won't let Nagelsmann leave before 2019, Joachim Low and Jurgen Klopp weren't willing to leave their teams. So they could either go for someone like Favre or for a promising but inexperienced coach like Kovac or Tedesco.
Anyway, this is an interesting appointment. Kovac has done a good job in Frankfurt. Though whether he's ready for the next step or not remains to be seen.