I've got to nominate The Matrix Trilogy, the second and third installments of which are, IMO, infinitely better than they're perceived to be and that I feel get criticized largely because general audiences and critics didn't/don't understand what the Wachowskis were actually intending to do with their narrative.
Although I've not yet seen the trilogy in its entirety, I know enough about where it ends up and have seen enough of the second and third films to confidently call the saga a genius subversion of the typical "hero's journey" narrative trope and the /"Western Superhero film" genre (not to mention a Transgender allegory, a Biblical allegory, and a Philosophical treatise as well), offering a hero who FAILS to accomplish what he's been told he's going to do/sets out to do and, consequently, something that is far more interesting than the myriad of other superhero films we've seen come out in the past 20+ years.