I'm all for the concept of Naraku seducing Akito's darkside. I like how Akito is having to live down all the bad karma she sowed in her former life, but at the same time I'm sympathetic to her and hope that she will be able to rise above it.

I think you are doing a wonderful job of blending the three fandoms together. Definitely Naraku's upgrades are as constant as Inuyasha's Tessaiga upgrades. So him being too much for them to handle feels plausible to me. The idea that he would want to feel off of Akito's negative energy and drain Neo-Queen Serenity's purity also sounds plausible. This story is very original and I look forward to your next installment.