Some things I didn't like about this movie
1. It rather unabashedly shoves theism down your throat. Instead of a balanced and thought-provoking discussion of theism and atheism, we get a theist making (poor) arguments for believing in a god (e.g. 'I want to believe it because that makes me happy', 'most people believe in a god', etc.) and the atheist retorting with "theism is silly" instead of critiquing his theist partner's arguments. As with other films, this one too portrays the theist as a poor victim being condescended to by a stereotypically smug atheist even though Carl simply wanted Assad to be rational and apply the same standard by which he found the Christian sect's beliefs absurd to his own faith. The film, instead of staying neutral, quite clearly implies that the theistic POV is more preferable than the atheistic one and stereotypes the atheistic worldview as too gloomy.
[Though I admit, the movie also portrays having faith solely in God as a bad thing when it shows how parents relying solely on God for help instead of going to the police when their kids get kidnapped are making a bad choice. Still, I felt that the film advocated being a theist (who doesn't totally rely on God and prayer) instead of not advocating any particular position and letting people come to their own conclusions].
2. Why did they make Carl homophobic? In the first film of the trilogy, The Keeper of Lost Causes (2013), Carl talks about the orphaned guy being homosexual and there is no hint that he has homophobic views. Yet in this film, we have him listing homosexuality as one of the "bad habits" he hopes people get over (implying that he thinks homosexuality is a choice and somehow bad). You'd think a film trilogy that tries to promote (by Western standards) a 'leftist' agenda (e.g. by trying to convince people to be tolerant of Muslims) would be responsible enough to not make homophobic 'jokes.' It soured the rest of the movie-watching experience for me when the protagonist I sympathise with turned out to be homophobic.