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That's a really great question. All three games are among the best ever made.

In terms of influence, I think Super Mario's move to 3D was the most successful. It led the great migration from 2D sprites to 3D polygons, and it influenced generations of 3D worlds. Ocarina, which built upon the foundation of Super Mario 64, was most successful in terms of overall game design. And Metroid Prime was most successful in terms of difficulty. In 2001-2002, there weren't many fans who thought Metroid would make a seamless transition from third-person 2D to first-person 3D. It remains, to this day, one of Nintendo's most impressive (and unlikely) achievements.