I don't know how you "reboot" something that didn't have much of a story in the first place. So I say stick with Metroids, and Mother Brain and all will be well. Trying to do too much and we know how that turns out.
With that said, I think the next Metroid should take a page out of the Bioshock book i.e. create the world or the unique atmosphere and let Samus run wild. Sort of like what they did with Echos, which was awesome. Then build the story around that world.
Personally I would like if they go to Mother Brain's home planet - if it exists in the Metroid lore.
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