Nintendo rejected concepts from F-Zero GX team at Sega for a Metroid game in the early 2000s, said Sega producer Toshihiro Nagoshi.
Not as egregious as Nintendo rejecting the idea of Samus fulfilling her profession. Retro Studios planned on having Samus fulfill more of a bounty-hunting role in Metroid Prime 3, namely, by having the player pick out actual bounties to go after. The higher-ups vetoed this, in part because of the genre shift for the series it would entail and in part because Samus doesn't really fit the role of bounty hunter to a T. The guys at Retro jokingly referred to her as a "pro-bono hunter" instead. There's also a story about how when Retro Studios made the suggestion, Nintendo's Japan-based officials were horrified at the suggestion of Samus becoming a "murderer" and being paid to do this; apparently "bounty hunter" wasn't quite the most accurate translation of their intended title for Samus Aran, which is ironic considering that her clearly stated mission in Metroid II: Return of Samus was to commit xenocide.
Sounds interesting, would of been good to see what sega brought to the table.
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