Keep in mind our mythology is a blend of exaggerated historical retellings, bland religious filler, and insightful allegories.
Try not to read too much into any particulars. Look at the myriad of names Odin has. The gods, much like ourselves, are a dynamic representation of a myriad of archetypes put forward in the form of stories.
Sometimes it helps to make cross cultural comparisons; Tiwaz is etymologically linked to Zeus and Deus. The Aesir-Vanir war has parallels to the war of the Titans where the Olympic gods overthrew an older set of gods.
Back to your question: Freyja and Frigg may be more like two sides of the same coin, as with Odr and Odin. I think the Vanir are generally symbolic of primal, cyclical forces and the Aesir symbolize higher aspects of the mind. There probably is some historicity to ancient tribal invasions. And sometimes stories are just stories.