I played both versions of Super Mario 64 on an OG3DS. AMA!

Super Mario 64 – 3DS Port

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Pros:

• Native widescreen support (with 2x resolution or Anti Aliasing as options)

• Configurable buttons

• Runs nearly full-speed

Cons:

• Chugs when things get busy (at least on an OG3DS, can't speak for the N3DS)

• Default button mapping may feel foreign for veteran players, and remapping the buttons is a bit of a hassle

Super Mario 64 DS

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Pros:

• Widescreen support (with a patch)

• Circle Pad support (with a patch) which makes movement much better than the default D-pad scheme

• Button customization (via Twilight Menu Cheats)

• Better Camera system than SM64

Cons:

• DS resolution is lower than N64, so the graphics are a bit blockier/pixelated

Verdict:

Both good games, can't go wrong with either. But some may not like the gameplay changes in SM64DS (which revolves around switching characters) and may prefer the streamlined nature of SM64 (where you play as Mario from beginning to end)