According to a pretty big german Nintendo magazine Eternal Darkness 2 will be developed by Silicon Knights and be shown this E3. They've been pretty confident for months now (saying that SK "strongly hinted" at it) and in the latest issue they had the game in their "E3 news" section - basically saying it will be shown, not stating it as a rumor. They flat out wrote "Silicon Knights will show Eternal Darkness 2 at E3 for Wii U". So in that case ED2 is out of the question for Retro.
The Starfox / Metroid Crossover doesn't make sense and neither does F-Zero (Sega made the last one and I doubt Nintendo would hire Retro to develop it since it doesn't have any sort of mass market appeal).
So that leaves us with Metroid, Donkey Kong or Starfox. Sales would suggest a Donkey Kong game but Metroid has a higher reputation among core gamers and Nintendo wants to make sure their console gets accepted by the core. Yeah I have no idea haha 







