SatAM was taking a, at the time, rather storyless project that was pretty light hearted in appearance to something a bit more storydriven and darker. Nintendo's would be Advance Wars Days of Ruin compared to the lighthearted Advance Wars series. Metroid doesn't fit as it was already dark.
I mean Samus has lights on her armor for a reason.
As for a Nintendo equivalent of SatAM, I'd be tempted to say Metroid, since it shares similar themes in its direction: morally gray technology, adventuring in an oppressive techbase, feeling of being alien and outnumbered yet heroic.