Do you seriously foresee some game in the form of Eternal Darkness becoming a huge million-seller on a Nintendo console? Retro working on another franchise like Metroid, Donkey Kong, Star Fox, Legend of Zelda, or even a Mech Rider/Startropics would be much more beneficial to Nintendo then a sequel or reboot of Eternal Darkness.
I say this as a HUGE Eternal Darkness fan. The franchise is just not going to sell a huge amount of copies on the WiiU or move a large amout of Nintendo consoles. If Nintendo really wants a "mature/core" focused game from Retro, let them create their own IP.
Retro has multiple teams now though, don't they?
And I mean...a hypothetical Eternal Darkness 2 doesn't need to be a $200 million cutting-edge production or something. A relatively modest production with some nifty Gamepad effects would be enough to appease the series' (admittedly small, but vocal) fanbase, show off some more of that asymmetric gameplay Nintendo's going on about, and
maybe attract some new fans (or some of the people ITT who've said they'd buy a Wii U for ED2). And it wouldn't need to sell a HUGE amount.
Anyway, all just fun speculation. I would really like to see Retro do a new IP, but I'm not gonna complain if they keep cranking out solid entries in existing series, either.
EDIT: just got your point about using valuable resources on unprofitable projects. I can see that, I suppose--though a smaller project in an unfamiliar IP might be a good way to break in some of the new hires without bogging down a bigger project...maybe.