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That depends on what you value:

-Graphics? The Wii version still looks better. However, you might have lower standards for handheld graphics than for console (especially if you don't own a Vita). Alternatively, you might not care much.

-Stability? Too early to say. The Wii version has some framerate issues, but those will probably persist or worsen on New 3DS. But maybe they'll surprise us.

-Portability? Obviously, only the New 3DS version offers this.

-Price? Well, the New 3DS version will probably cost you a bit less ($40) than the Wii version, which typically costs $50 at a minimum. However, the New 3DS version requires buying a new device... So factor in that cost if you weren't going to get a New 3DS anyway.

-The Dolphin factor? If you hook your Wii up to your PC and use the Dolphin emulator, you can get the best graphics/stability by far.