One level of auteur theory that I've wondered about is its political ramifications. For one, it's not a very communist theory. There's no real collectivism or equality in the idea of a singular mind behind a film. Which is probably why Godard (partially) rejected the theory later in his collaborations with Gorin. Also why Third Cinema purposefully distinguished itself from the tradition of French New Wave (a tradition of un-quality?) by categorizing it as the "Second Cinema".
Likewise, auteurship was and is a title mostly populated by white, male directors. Oh sure, there's a few notable exceptions: Agnes Varda, Claire Denis, Ousmane Sembène, etc. Nonetheless, it's important to question whether auteur theory succeeded due to the power already allocated to the canonically white, male director. And whether auteurship erases the contributions made by the editor and screenwriter, positions usually more diverse in gender and race (for instance, Marcia Lucas in Star Wars and Taxi Driver).
Personally I view auteur theory as a necessary weapon against the studio system and against the "tradition of quality", but not necessarily a theory that reflects the state of an actual film production. Truffaut, Godard, et al used it as a banner to wage war against the powers above them—producers, financiers, etc—but in doing so they also negated the work of those below them, the grips and gaffers, the cinematographers and editors. I don't believe this was their intention, but hey, they did make a theory about how filmmaking is all one dude's creation. Not exactly hard to see how that'd ignore other people's contributions.