What makes you so sure they ever even approached Nintendo about making an Eternal Darkness 2? This is Dennis Dyack we're talking about here, the guy who ditched Nintendo because of the Wii.
If Nintendo's relationship with SK was as good as I hear it was, I can't imagine they'd refuse if Precursor went to them with an ED 2 proposal. They'd be crazy not to offer to publish it, and if they did publish it I'm sure Nintendo would offer the same QA they did the first time around.
The rumor (I know, rumor, but they seem to have been pretty accurate from certain people) was that they went to Nintendo with it, but it would've taken an extra $10m just to keep SK open in addition to the game itself. A similar situation to that of Factor5 before it closed.