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It's hard to compare the two games. They are both part of the same series but they play vastly different from each other. Super Metroid is more fast paced with an emphasis on platforming while Prime is much more slower paced and focuses more on exploration and shooting. Both games are equally amazing and it really depends on your preference as to which is the "better" game.

I prefer Prime because the first person view and scan visor add a rich layer of immersion into the game, but I still consider Super Metroid to be one of the greatest Metroid games.