I really like what was said earlier about building upon Super Metroid in a way similar to how it built on the original Metroid. No narration, complete isolation, and expansive caverns are a good place to start.
Instead of strong black shadows and a cel shaded style, how about a hand drawn comic style with subdued shading, strong attention to detail, and a colorful, alien pallete? I'm thinking something similar to Sam Kieth's version of hell from the beginning of Gaiman's Sandman. Add a really stylistic flair to Samus' animations and abilities as I believe that could really work in the games favor of adding the main characters mystique. I don't mean making her do everything in an over-the-top fashion either; in fact almost the opposite. Instead, animate her in a way that really accentuates her nature as a cold bounty hunter(as well as building upon her mysterious mythology) with slightly stiff and unnatural movments.
Save the over-stylized effects for the suits more extravagant powers. For example, Shinespark could kick up an impressive amount of brightly colored dust and pull the camera back as she launches herself through cavern walls and enemies. Something like Crystal Flash could also send out a shockwave at the end, obliterating enemies in a way similar to the Power Bomb.
I think it is also important to stay away from context-sensitive actions. I don't have the hatred for Other M that some fans do (even if I agree with mostly every criticism, aside from those about the first person switching and controls), but I definitely think that adding such actions simply serves to pull the player out of character. Valve's philosophy of not taking control away should apply here, as I believe it can be really helpful in creating immersion.
