I liked the idea behind Other M. Portraying Samus as broken was quite interesting. If I wanted to focus on story, that's the direction I would like to see Samus taken. Better execution and more clarity, of course, but the same source. In a way, it reminded me of NGE. Focus the story on Samus trying to hold it together. To explore her character, have the story start with her being hired to protect a frontier colony. Set it in first-person in town and first person in missions. Make Samus scary as fuck to the average person.
If I wanted to make a game more focused on gameplay, I would go for third person silent Samus. Put the effort of story and characterization into world building. Lots of environments with exploration. In this one, instead of having one planet, put her in her ship and have her work for bounties. Give her something to chase like for an overarching story. She can dock and receive bounties and purchase upgrades on her weapons. Really focus on the weapons. Make a lot of gunporn and upgrades to really emphasis her mercenary status. Have a bar where she can get missions from more morally gray sources. Then, when she gets a mission, you fly in on a short rail shooter section in your ship to your landing zone where it opens up to a more tactical setting.