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The list of nominations has been cut in half as Pokémon Uranium and Project AM2R are removed from the Best Fan Creation nomination at The Game Awards 2016. Without announcement of the removal of both titles, fans still noticed.
Both titles were removed from their web sites after Nintendo sent a takedown request under the DMCA to both creators/programmers.
Pokémon Uranium was a fan-made PC game, while Project AM2R is mainly a remake of Metroid 2. Of course, Metroid and Pokémon are properties of Nintendo, which may be the cause of the removal from The Game Awards.
The original list included Brutal Doom 64, Enderal: The Shards of Order, Project AM2R, and Pokémon Uranium. Only the first two mentioned titles remain on the list.
[Source]: NeoGAF: AM2R and Poke Uranium Both Removed From the Game Awards “Best Fan Creation” Category.