How much will you have to change to avoid Nintendo DMCA on Hiveship and Phazon? Can you get away with just not mentioning trademarked names or will you need an entirely new main character and model?
Asset-wise, building an entirely new model. New face, new hair, new outfit. I will recycle the body built for DazV5 Samus, and the new outfit will still be a skintight suit, pulling inspiration from things like the Crysis Nanosuit and the Battlesuit from Resident Evil 5, while also pulling influence in from bondage outfits and shibari designs.
Story-wise, very little needs to change. The formerly-Phazon hexology will need a new name for the substance being experimented with, but that won't be difficult, because it being Phazon as described in the Metroid Prime lore was very tangential anyways. In fact, Metroid lore snobs probably rankled at the use of Phazon, since supposed it was all destroyed by the end of the Prime trilogy. This was going to be handwaved away in later episodes, but now I can engineer a substance where that isn't an issue at all.
Virtually nothing at all changes with Hiveship. Its ties to the Metroid IP literally went no further than the names of Samus Aran, The Galactic Federation, and Phazon. It was otherwise an entirely original IP anyways - and now, it is an entirely original IP.