What was the point of all the suffering? What was the intended message here?
The discussion will unavoidably be full of spoilers, in case you didn't watch the movie yet.
Historically, their efforts and suffering were basically for naught - christianity didn't really make a dent in Japans history or belief system. Their numbers are insignificant today. I even feel like non-christian Japanese might not feel good about how naive or gruesome most of their countrymen are displayed - they will probably reject the movie as it is. Those that are already christian might see some purpose in it. So its message is not really about proselytizing then.
I understand it was a passion project for Scorcese. So is it more of a spiritual journey intended for christian viewers? If you look into the eyes of both missionaries in the beginning, they seem really frail and child-like. And throughout the movie it doesn't seem like they will ever become men. They never succeed in really teaching the evangelion, they don't attempt to explain heaven to a husband and his wife - they just leave things as they are. It leaves the impression that they left the Japanese christians - with their really basic understanding of christianity - before they physically leave town. One of them dies in vain rather quickly (not in the runtime sense): it was an honorable thing to do, but in vain nonetheless. He couldn't save the Japanese and he couldn't save himself. Neither in the spiritual, nor in the physical sense, I feel.
The other one even gets humbled by getting told that he shouldn't compare his insignificant suffering to Jesus.
Throughout the movie - until the very end - he gets continually mentally tortured by the man that brought him to Japan. A direct consequence of him never attempting to teach him what forgiving and sinning even is. There is no attempt in correcting this and I don't think that he ever understood what's wrong about this.
So what was the intended message? God won't answer most people? Suffering is part of life and you should read the book of Job again? Someone who is more versed in the bible teachings will probably see more in all of this - I'd be interested in hearing it.
The ending sequence is almost insulting in how little it trusts the viewer to draw his own conclusions - it really diminishes the impact of the movie for me. Normally I'd watch a movie again if I feel there's something else to it - but Silence is way too drawn out for that. As a movie that stands on its own, I wouldn't know to whom I could recommend it. It can't help christians in doubt, it's not intended for proselytizing, as a historic film the characters are not fleshed out enough even though the acting is good. The purpose remains unclear for me.