I think you know this isn't true.
He's played 45 and 48 matches in the last two seasons, so its not like he's not played at all since the time he got there. Now, he's been injured for a while and they've brought in a few new wingers who've done really well without getting rid of anyone else so he can't even get games out of position.
Guardiola has been unable to recognize that he isn't a winger, and its hurt his development that his coach can't even properly spot where he plays the best. He has had some patchy form the last few seasons, but thats typical of younger players.
Bayern mostly now plays with two big strikers in important matches, and they are two of the first names on the team sheet, so getting in the lineup at his main position isn't all that easy, considering he's not that style of player and Muller and Lewandowksi are two of the best strikers in the world.
I don't think this is what he chose. I think he's been unlucky to miss so much time with injuries and unlucky to have a manager that has hurt his development. Is that his problem? Should he have known this would happen? You sure you aren't saying this only because you are a Dortmund fan?