I think Herzog, in his dark German heart, isn’t describing the 3-act structure as in “Beginning-Middle-End” (Aguirre has a beginning, middle, and end after all) but a particular 3-act plot in which the protagonist undergoes a change / arc. His point is that the protagonist doesn’t have to change, and certainly not for the better, in order for the film to tell a good story. Aguirre doesn’t change. The rebellious dwarfs in Even Dwarfs Started Small doesn’t change. Stroszek DOES change, and it’s the closest to a Hero’s Journey that any of the Herzog films I’ve seen do come, although it’s a negative arc — Stroszek loses his innocence and gives up on his quest at the end of the film.

In responding to your question in another post about Hero’s journeys that don’t require a physical journey, I started going through movies I’d seen, and I noticed that certain directors don’t opt for Hero’s Journey storylines / archetypes much if at all: Herzog, Polanski, Kubrick, Welles, Renoir, Bunuel…. Now these aren’t the most mainstream Hollywoodish of directors, but other directors who appeared to adopt a positive transformative arc in Hollywood fashion actually suggest problems with the model or even subvert it (Nicholas Ray, Douglas Sirk, Paul Schrader, and a boatload of film noir directors).

So I agree with Herzog that one can avoid the typical Hollywood trajectory and still tell a compelling story (if not necessarily a profitable one — European financing differing markedly from American financing of course). A number of the AFI / WGA top 100 scripts of all time have negative arcs or no arcs for their protagonist.

But I don’t think Herzog is correct in blaming the 3-act structure or a particular subset like the Hero’s Journey for bad storylines. A number of directors / writers have crafted unique but compelling stories that actually follow the traditional outlines of some 3-act structure or another (Linda Seeger has pointed out that the plots of Memento and Mulholland Drive are actually fairly conventional).

And other directors / writers adopted a straightforward, conventional plot type and still performed marvels by staying true to their unique vision (Capra, Hawks, Ford, Wilder, Penny Marshall …). It all depends on the writer’s goals and skills.

It seems to me that the concept of a 3-act structure is most helpful to writers in analyzing shortfalls in their own storyline. For example, in most of the hundreds of scripts I read on a peer review site, the plot fell apart somewhere in the middle. The easiest way for me as a reviewer to describe this problem to the writer was to refer to the midpoint of a 3-act structure. Other stories had the problem of not getting started (i.e. of not engaging me as a reader) until somewhere around 40% or more of the script. Again, it’s more helpful for a reviewer to talk to the writer about a plot point at the end of the first act when the protagonist commits to a quest, after which the main action / conflict should commence, than to say simply “Your script takes too long to get started.”

I use something like a 3-act image / gestalt / division in my head as I write, but if I ever felt the need to try something different, I wouldn’t hesitate to do so, and then I would get feedback from good readers to make sure that the variation / aberration from the norm did actually work.