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On a smaller scale, I'd say Metroid: Other M.

Think about it. It went against what people knew about the series with a cinematic approach, was developed by people who had never before made a Metroid-like game, involved putting one of Nintendo's most legendary series in the hands of outsiders, and essentially attempted to simplify the controls of the modern action game into something that could have been done with an NES Gamepad and Zapper.

Say what you want about the end product, but even making it involved some courageous risk-taking.