I've seen it twice and admire it deeply. This is a film with high ambitions and I gotta say it's a grower. What it does in terms of conveying an inner spiritual struggle with such strong cohesivness is something to enjoy and admire. There are plenty of inspired moments of quiet transcendence (what about that brief yet powerfull completely silent bit when one of the japanese sees the crucifix and is moved to tears by it's sight?). But this is no picnic. And to be honest I'm still struggling with Andrew Garfield's performance, which is not really only a performance problem but a direction problem (I guess). Maybe that's the point, but all three main characters in Scorsese's religious pictures (Last temptation, Kundun and this) are so involved, or should we say self involved in their spiritual and faith related inner struggles that you can't get to know them at all outside of them. In the rest of Scorsese's filmography, personality traits and character idiosyncrasies always nurture the total portrait of these human beings, but not so with Jesus, the Dalai Lama and father Rodrigues. The thing is that the first two are religious icons, and their mystic nature may be justified, while Rodrigues is a "normal" human being, yet I don't know if he is insecure, if he has a sense of humor; he's dead set on this faith mission, and barely utters a word about anything else.
Experience tells me this perception will not change, and that this is the way the character and the film are constructed. It's a bit of a shame if that's it, cause when Liam Neeson appears, he injects a lot of gravitas to his character, and he manages to give more layers to HIS dilemma than Garfield does. However, the film is too dense and packs too much for me to be able to say with all certainty that any of this is set in stone. I'll have to see it a couple more times to re evaluate.