"Naturalism presumes that there is no God, or other super natural agents that transcend nature."
In searching about for a proper response to your post, I came across an interesting article. In a nutshell, the contention is that if you want to talk about thinking, it is necessary to think about talking.
This is a long article, but it is surprisingly rewarding. I also feel confidant that you will learn a few new words, as well as a new way of looking at a few things. You'll be surprised at which names and historical events get mentioned.
Initially, I researched Naturalism. I can see why you think it is a limited philosophy. It is by definition a limited philosophy.
Then I went looking for Scientific Empiricism. Gradually I came to a focus on the linked article. This is interesting stuff. Try not to discard it as too convoluted, off the subject, or difficult to understand. After all, if this can exist in our world ...
... then such as the rest of us can comprehend the meaning and import of the article I linked.
Where does it lead?
To the question why Plato had not developed science, ... because he got things backward.Later, speaking not of Plato, but of the author of this philosophy ...
... Plato started from rhetoric, which had displaced myth and poetry as processors of knowledge. But rhetoric was based upon persuasion in the vernacular. ... Consequently it was unsuited for dealing with the Form of wisdom in the realm of Idea.
... he was looking for rules for the behavior of phenomena rather than causal properties of matter as such..
Anyway, this is going to require a great deal more study and reflection, for me as well as anyone else who wants to follow these faintly echoing footsteps.