The reason Dark Souls works is due to it being multiplatform in nature; it targets a very specific group but that group is across multiple consoles, so that can lead to the series having successful sales and thus the investment in the series being worthwhile due to it being on mostly everything

.
The issue with Metroid in this case is that it would be Nintendo exclusive and because of that it will only land on a few devices (Wii U, NX, 3DS). And out of all of them, the 3DS is the most successful.
Logically, you make a Metroid game on that, but most hard-core Metroid fans would want a grand AAA adventure to make up for Other M (and I would like that at some point honestly

).
But Nintendo isn't made of money and they are likely saving the next console Metroid for their future home console. So what does that leave the 3DS with? A few things; they could make a 2D Metroid like past handheld installments, a FPS in the style of Hunters, a 2.5D title like Next Level was originally pitching or something completely different.
Nintendo chose the 'completely different' option and....people are mixed, to put it lightly, toward that move.
I guess Nintendo could make Metroid a niche franchise, but I don't expect them to; they want it to be a big seller like Zelda and Mario. But if they want to be true to the series, its likely it will never be that big seller, but they refuse to accept it.
It will be interesting to see where the franchise goes once the NX is announced honestly.