Geoff Keighley recently unveiled all of the categories and nominees for The Game Awards 2016, including the "Best Fan Creation" category. Two of the nominees for this award were fan-made games that were struck down by Nintendo: AM2R: Return of Samus and Pokémon Uranium. Now, just three days after the nominees were posted, the website no longer lists either of those games, and it appears that they have been pulled from the show. Only Brutal Doom 64 and Eternal: The Shards of Order remain for that category.
So far there has been no official word from Keighley explaining why these games were pulled from The Game Awards, but the most likely answer is that Nintendo intervened in some way. The creators of both fan projects received DMCA takedown requests from Nintendo, and Uranium's developer was even reportedly threatened with a lawsuit in the hundreds of thousands of dollars. It's not much of a stretch to assume they wouldn't want these games prominently displayed during an awards show.