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Well the levels are stored on Nintendo's servers. You can see them all on the Super Mario Maker bookmark site. You can link your NNID from Wii U to the Switch, surely they could have found a workaround for this. The 3DS levels are irrelevant because you could never upload those online anyway.
Either way, it's not a deal breaker for me because I didn't expect they would be carried over. What I'd rather see is for the next Animal Crossing to allow us to import stuff from the previous game. I think that would be more useful than this.