The issue at Bayern recently seems to be clear as day. If Pep has ever had a fatal flaw as a coach and tactician it would be that he is willing to sacrifice balance in favor of control.
It's clearly visible in how Bayern transition up the field. When they build from the back, everything is orderly and smooth. As they build into midfield, all players have great connection and the shape works well. Their transition severely decelerates when they reach the final third and they start piling up and playing slow in front of the box. Slowing down like this causes the midfielders to be dragged out of position and all defensive security to be lost.
The gap between the backline and the rest of the team becomes massive due to this and leaves plenty of space for teams (Real) to set up a counterattacking chain. Having guys like Boateng and Dante alone and uncovered at the back during a quick counter is asking for them to be slaughtered when on the back foot.
Things changed drastically today when Bayern stopped trying to 'force' the possession game and went on the instinctive Heynckes-profile quick penetration in the final third. It went from 1-2 to 5-2 and could've been well more. Pep's system in midfield works wonders but Bayern need to utilize the same tempo when they get into attack as they do when building up. If they keep compressing their team shape the moment they get to the box, they'll never find an opening and leave Real to toy with them with counter after counter.
Balance the attacking phase with every other transition and Bayern should be able to beat RM with a decent scoreline. Placing Lahm at RB and Martinez at DM helped to achieve this. Please do not fuck up and hand RM a great chance to win La Decima.