There have been massive overreactions and overassumptions because of the loss but Pep was annihilated today, no other way of putting it. The disrespect he's getting is kind of surprising though, coming from cules.
Of course, this is the opportunity for underground haters to rise up and voice opinions they held back while he was successful.
He needs a tactical growth. If he's going to stick with his philosophy, he's going to have to take an approach FAR different from what he's done today (nightmare choices). Mandzukic is nothing but a 'wait for the ball' target man who doesn't participate in any team transition, disrupting unity which should be and always was a key part of Pep's system. Sticking physical yet not technical players like Schweinsteiger and Kroos to run a midfield that's trying to dominate a game, having no DM to give a natural balance, etc. All of these are horrible decisions.
Bayern would've been much better had they fielded a trio of: Kroos-Martinez-Lahm or if he hadn't gotten injured, Thiago-Martinez-Lahm. Schweinsteiger is in total turd form and in all honesty, is much more of an engine for vertical attacking football than the base for tiki-taka. Lahm has the workrate and technique to succeed in a box-to-box role but as a lone CDM to give a backbone to play? No way. Martinez gives this in a 4-3-3 (or 4-1-4-1) and that would be the most balanced Bayern side (with a lot of other improvements though).
And to those who talk about tiki taka being dead are really not disproving anything except for the fact that possession football is dead. Sure, Bayern play with a lot of short passes but to actually classify that itself as what made the Barca system so successful for 4 years is ridiculous. The fact that the midfield setup was completely wrong and screwed them in both attack and defense only tells part of the story. Over the past month, Bayern's attack phase has turned to fuck all. The moment they reach the point where they should accelerate to create chances, they turn into a line of midfielders behind RM's midfield shield + lonely Mandzukic way up top serving no purpose. The fact that they break shape like that shows some sort of dysfunction in the attacking system. The slowing down also forces them to commit too many players forward and leave a backline to get slaughtered on the counter. Issues arise all over when a team doesn't stay true to their team shape, hence being tactically outclassed by Ancelotti and Madrid.