Since then they have become almost a pure possession side who have become easier for top top teams to play against and break on.
Problem is Bayern aren't good enough to play like Barca did, except in the games vs inferior opposition. And that's the difference. Pep espects the same results with lesser players. He plays the same way if he has Alves on the right, or Rafinha. If he has Xavi in midfield, or Thiago. Messi, or Muller. Bayern has a great team, but if we compare it to the team Pep had at Barcelona, it's just not as good, and therefore, not capable of winning in the same fashion which was typical for Pep's Barcelona team.
This Bayern does look like Pep's Barca against smaller teams, at home especially, but not against bigger guns, because the players he has in Munich, while great, do not allow him to control games like his Barcelona did. You can't find better passers and dribblers than Xavi, Iniesta, Messi, Alves etc. on their positions. Not in Munich and not anywhere else on this planet for that matter.
You switch Messi with Goetze or some other player, Xavi with Thiago, Alves with Rafinha, Busquets with Xabi Alonso and such, you're gonna have a worse team. Simple. Pep needs to learn the players make the difference as well, more than the manager in most cases. The players he had at Bayern couldn't play the Barca game like prime Barca players did. It's just like expecting some X-Factor contestant to sing a Whitney Houston song as good as Whitney herself. It's just not possible. Both him and Bayern's bosses should have known such a simple fact. But Bayern were probably infatuated with the way Barca played under Guardiola, that's why they moved for Pep.