An uneven and incomplete structure delivers an unclear message.
Roger Ebert, in his review of The Master, notes:
"The Master" is fabulously well-acted and crafted, but when I reach for it, my hand closes on air. It has rich material and isn't clear what it thinks about it.
The phantom meaning Mr. Ebert refers to exists because the film itself fails to offer an Objective Story Throughline.
Every great story consists of 4 inter-connected parts: a Main Character Throughline, an Influence Character Throughline, a Relationship Story Throughline and an Objective Story Throughline. Each corresponds to a different point-of-view the Author offers on the story's central problem. The Main Character grants the 'I' perspective, the Influence Character the 'You' perspective, the Relationship Story the 'We', and the Objective Story gives us the 'They' perspective.
The Master lacks an objective view.
As such, we get great insight into the issues of Freddie Quell (Joaquin Phoenix) and Lancaster Dodd (Phillip Seymour Hoffman) and the Relationship between the two of them. But we only get an occasional taste as to what 'The Cause' (Scientology) really is and how dealing with that interacts meaningfully with the aforementioned personal drama. Of course, doing so requires judgments to be made on that particular subject matter and and the consequent protracted lawsuits that many have faced doing so in the past.
Narrative Science (and the theory of Dramatica from whence it came) doesn't exist to provide a formulaic step-by-step approach to writing a story. It exists to help identify the nature of the holes within a work of fiction and how best to address them.
Ebert concludes his review with this:
"The Master" shows invention and curiosity. It is often spellbinding. But what does it intend to communicate?
Crafting an Objective Story Throughline would have provided the Audience with a much-needed objective view and the meaning Ebert so desperately wanted.