There are already various books and collections that are selective about which suttas they contain. As I recall Thanissaro Bhikkhu’s Wings to Awakening concentrates on liberating teachings. Bhikkhu Bodhi has a collection The Buddha’s teachings on social and communal harmony and In the Buddha’s Words is a nice collection that puts the various categories of sutta in context: https://readingfaithfully.org/in-the-buddhas-words-an-anthology-of-discourses-from-the-pali-canon-linked-to-suttacentral-net/
Personally, I’d rather try to approach the text on their own terms, not trying to shoehorn them into a scientific world view. Story telling is an important communication form in may cultures, particularly ancient indigenous ones.
Some material that has helped me with that was Bhante Sujatos talks:
And Rita Gross, who taught both history and Tibetan Buddhism:
[quote]Historical consciousness and traditional Buddhist narratives
…
I will discuss how the mythic account can be interpreted symbolically and will argue that symbols should not be considered as less important or real than facts. Only those who buy completely into the model of scientific materialism provided by the European enlightenment would not understand that in religions, symbols are as meaningful as facts.
[/quote]
There is a nice series of talks here: Buddhist History for Buddhist Practitioners Dharma Seed - Rita Gross's Dharma Talks at Common Ground Meditation Center