In my opinion, the reason that most Nintendo fans don't want Metroid Prime to be considered a FPS is because of the stigma attached to the genre. Many people consider FPS to be brainless, but his isn't necessarily true. It's just true of most of the modern FPS.
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Tag "Sorry man. Someone pissed in my Wheaties."
"There are like ten games a year that sell over a million units." High Voltage CEO - Eric Nofsinger