Müller literally finished in the Ballon D'Or top 10 multiple times and even finished in the top 5 in 2015 ...
You're seriously overrating the "flashy part" of the game.
When he's on top of his game and used correctly, Müller is a top 10 player in the world.
You are right in one point though: The system is important for Müller, which is why he's so unique.
If you have coaches, that don't know how to use him, he will be solid, but not that special. However, if used correctly, he's just incredible. Let's take players like Coutinho for example. In a standard team with a standard coach, he'll probably function a bit better than Müller. If you have a coach, that knows how to play Müller, the latter will easily be better and more valuable than Coutinho.
His qualities are just too hard to quantify for most casual fans and sometimes even coaches. He might not "look" like one of the best players in the world and you might personally dislike him for some reason, but he is outstanding and unique.
Almost every single metric, like the one that
@Blackwidow showed you above, supports that.
Heynckes himself raved about Müller in an interview today btw.