I’m very interested in the idea of Egyptian mythology reflecting its history, like how Horus originated in Nekhen/Heirakonpolis and Set in Nubt and came to represent Upper and Lower Egypt. And how Horus and Isis we’re incorporated in later. I want to understand the original forms of these deities and their associations and how they developed into later forms.
Wilkinson's Early Dynastic Egypt is the go-to resource for early Egypt. He has a section on gods in the chapter on cults and shrines.
There have been several monographs that study single deities from a diachronic perspective, such as Turner's Seth: A Misrepresented God in the Ancient Egyptian Pantheon?, Following Osiris by Mark Smith, Hathor and Thoth: Two Key Figures of the Ancient Egyptian Religion by Claas Bleeker, and Holger Kockelmann's masterful Der Herr der Seen, Sümpfe und Flussläufe: Untersuchungen zum Gott Sobek und den ägyptischen Krokodilgötter-Kulten von den Anfängen bis zur Römerzeit, so I recommend taking each deity individually if you are interested in their origins.