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They look almost identical! The only two things I noticed were the 3DS didn't have as much detail as the Wii version with textures. (the wood on DK's house had a more detailed texture on the Wii version). The other thing I noticed was the background (past the first layer or two) was less detailed)
Honestly, the rest of the game seemed identical to me. The 2 things I pointed out wouldn't even be noticeable without this comparison video. They did an unbelievable job with the visuals on this game!