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I thnik Nintendo did it the best.

To make the BEST 2-D franchises (Mario, Zelda, Metroid). Then transform them into the BEST 3-D franchise is no easy feat. I think games like MGS made the transition because the 2d ones weren't exactly great (IMO).

the 3D games being better than the 2D games doesn't need to be a requirement, plus how can you top games like Super Mario Bros. 3, Zelda: ALttP, and Super Metroid, But i'd say Metroid Prime, Mario 64/Galaxy, and Ocarina of Time did a wonderful job living up to those games since all 4 are in the top 10 highest rated games ever made.