I'm still mulling this one over, so I'm waiting until I arrive at a conclusion to post my full thoughts on the film. This will likely require another viewing, but I'd like to address some of polkablues points.
I think your analysis is pretty good, polka. I agree that Doris is really the key to understanding Freddy. However, I don't think he chooses not to return to her after the war because "he's too fucked up from the war". She writes him during the war, stating that she is moving on. This is what fucks him up. This is the initial trauma, and it's so strong that it renders him incapable of coping with both subsequent traumas as well as the previous ones, namely the war and his family.
I also think you're on to something when you write about the reaction of Freddy to Kevin J. O'Connors criticism of the Master's work. But I think this scene is part of a bigger underlying pattern in the movie. Whenever the Cause is questioned in the movie, that criticism is always ultimately met with raw, emotional rage by Freddy or, more importantly, the Master himself (I'll return to this later). This is a manifestation of cognitive dissonance. They both know the criticism is true and that it cannot be countered with reason. The only defense left is dumb, animal rage.
I think you're totally right about the motorcycle scene. But, again, I disagree with your analysis about Freddy's return to the Master in England. I don't think it's out of affection or "nostalgia", but a genuine last ditch hope that the Cause offers some cure for his deep emotional and psychological wounds, and primarily, something that will truly fill the void left by Doris. He's begun to face it, but he's still looking for an easy way out.
In England, Freddy is initially receptive to the Master, even after being berated by his wife (it is here he finally glimpses the true nature of the Cause). When he and the Master are finally alone, Freddy asks him if he can really cure mental illness and where they first met. When the Master starts going on about meeting in former lives as Prussians during some old European war, Freddy detects the falsehood and it is AT THIS POINT that Freddy's faith in the Master is completely snuffed out and he sees him now as a man -- a man as lost as he was. As the Master goes on and on, and his bullshit turns to desperate yearning you can see that Freddy's idolization turn to pity.
But the film is called The Master, not The Freddy, and I think the movie is really about the Master himself. He is not, as many have put forth, a charismatic master manipulator. He's a self-conscious fraud. Even his children ultimately desert him. He's a man as tortured as Freddy, but he's been anesthetized by the Cause. He's infatuated by Freddy because Freddy is pained with real pain and the Master yearns to feel something real. He is drowning is self-delusion, guided by others, just as much a cog in the machine of the Cause as any new member. The jerk-off intervention scene with his wife isn't about Freddy at all, but about the Master. He's drinking Freddy's hooch, drifting away into Freddy's pain, touching his own dormant pain, and relapsing into his true self. He's trying to find an escape through Freddy, but the Cause (his wife) yanks him back, literally.
Those great processing scenes between Freddy and the Master are not about curing Freddy at all, but about the Master curing himself. In his reaching into into Freddy, he's really reaching for something real and raw, something he hasn't been able to feel in a long time.
During the speech at his daughter's wedding he talks about marriage being unbearable before the Cause. He then talks about lassoing the dragon and putting him on a leash. His next step is teaching the dragon to play tricks. Well, the dragon is reality. And I think if this movie is a criticism of Scientology, this is it. Scientology is heavily critical of the field of psychiatry and their, what Scientologists see as, predilection toward medicating. Instead, Scientologists seek to cure people's psychological afflictions with their own mumbo jumbo, something very similar to the Cause's. At it's essence, this mumbo jumbo is self delusion. Their lassoing of the dragon is an attempt at deluding one's self into believing unpleasant realities aren't real, but mere reflections of past lives, etc. The Master says that before the Cause, marriage was unbearable, but now the things that made it unbearable are suppressed, ignored, imagined away. But at the end, they're still there. And they're on a leash. A leash is a connection to you, not a barrier. What happens when you put an animal that wants to devour you on a leash? A lot of running?