Thank you for sharing your thoughts. There is absolutely no way one can read any prophetic book and not come away with the notion of judgment, either on the Israelites or other people. Your use of Jonah stands out to me as a classic example of judgment being brewed against a nation other than Israel. However, the happenings of Jonah also make me see some themes of repentance which brings about mercy and compassion.
My reflection about wisdom literature was limited to the view of it being mostly about human experience and how to live the full life. I did see that how people are spoken to, to live as God desires. However, your mention of the concept of relationship between God and nature is interesting. The psalm and other wisdom books are replete with such imageries. Although it does not so much talk about how God, speaks to the people as in the prophetic sense, it does display a relationship between God and nature.