I met three priests in my life. Met as in had an actual conversation and heard how they talk with others and not just saw them performing rituals. I met a bishop, a priest who was a member of a commitee in charge of the retranslation of the Bible and a priest from a small settlement. All of them struck me as smart, learnt, knowledgeable individuals skilled in rhetoric.
What I know about priests of the past is that they continuously struggled with faithlessness and heretic thoughts. Sometimes even themselves questioned their own faith as a test of their believes and they made an effort to prove things like existence of God as Thomas Aquinas did. They participated in religious debates among themselves as a part of their education. They knew all the weak points (which could be anything really) of their beliefe system and they were capable of defending it sometimes even with sophism. Jesuits were the cream of the most educated priesthood and in reality of course lot of the priests weren't that much paragons of knowledge and intellect one could be fairly sure that Jesuits were made of quality material.
The communism despite it's best effort (like socialization of schools and banning religious education of the children) could not break the church because communists knew nothing about Christianity but the priests read Marx and Lenin and they knew all their teachings and could show the Christians the shortcomings and contradicions of this ideology and the corruptness of it's leaders and advocates.
Compared this the conversation, the debates and the arguments in the movie are... well... pathetic. It feels like as it's what a modern faithless and godless man (who only knows memes about Christianity like Jew on a Stick or Flying Spaghetti Monster) would think about what a priest would say when they question their faith and effort of converting others to their faith.
Like when Liam said that the Japs isn't worship God as they do in Europe but some caricature so it's better just to give up a real priest would reply for example that this is all and well, this is just the beginning, the work is long and never ending to chisel the misunderstanding and shape their views better and bring them closer to our belives. First to grab the Jap's attention we need to focus on small things, small and familiar things which are similar in both cultures. Let them think that the God is the Sun who resurrects every day, we already met with similar thoughts, the cyclic nature of nature, we already met with similar religions, like the worshippers of Osiris, we already met the heretical thoughts of gnostic Christians about reincarnation. It's nothing new to Christianity and we, the Church, already have the answers to these kind of challanges, we have the means to correct these mistakes, and we will aply our knowledge and experience, so, dear Liam, please go and fuck yourself. I would expect something along these lines.
Yes, ultimately the missionaries are failed in Japan and Christianity remained a niche religion and I don't expect to change the movie as if they were triumphant but such cursaders of the faith like the Jesuits who wield will and words instead of shields and swords I would depict them with more spirit in their struggle.
Then in response to this the Buddhists could have react even more cleverly. With the resources Scorsese has the movie should have had a bit more dramatic punch but it's just lukewarm.