The only way I'd consider the 3DS the Wii U's worst enemy, would be in that when Nintendo should have been ensuring games like Pikmin hit their deadlines, they diverted all their resources into the 3DS to save that instead.
Now you've got the reverse with the 3DS having much slimmer pickings whilst most of Nintendo's resources are being pumped into the Wii U, however the 3DS was lucky, while Wii U's reputation looks to have been irrevocably damaged to the point where it doesn't matter what Nintendo do now.