You don't have to believe everything he says. 2011-12 side was a work in progress with lots of new ideas being implemented, I still rewatch some of their games and see it as an (yet) unreachable benchmark. It's an open secret that Pep has left due to the Board. He couldn't bear the rats who marked the start of their tenure by stripping off honorary presidency from Cruyff.
You also forgot to add that Bayern refused to get Pep 'his' players (Thiago being an exception) and sold Kroos. Buying Vidal against his will was probably the last straw.
I honestly think that dealing with the boards was the main challenge in both clubs, he doesn't seem to have such obstacle here. He'll stay for a long time, the only other high-profile club suiting him is Barca after all. I would go even farther and say that in ideal case Pep would enhance his influence over youth teams and wait for the academy products to ripe - the luxury his teacher was denied. Cruyff needed to wait 20 years (1988-2008) to see his La Masia conquering the world, so would Pep. Guardiola is not a lone revolutionary as it's sometimes represented by media, he steadily develops the concept of his teacher. This concept needs time and patience, and who bar City can provide a background for such mammoth work right now?
About the first - that is what he always told. There might have been more reasons but when you see how intense he works he might be right.
The board was not the problem at Bayern - especially as Hoeneß came back with whom he is big friends. And he and Reschke - the guy who manages the transfers - only talk big from each other. Bayern has a special philosophy with players - but I somehow have the feeling that Pep and Bayern weren't far from each other when it meant players. That was not the problem. Do not forget that Thiago was on the bench a lot in his last season and Vidal played.