I don't really think Gunpei Yokoi needed vindication, with him being responsible for the Game & Watch, the D-Pad, Metroid and not to forget the GameBoy itself I'd say he'd earned his stripes. Virtual Boy doesn't really diminish his accomplishments. Besides, wasn't he opposed to the release of the Virtual Boy as it was, because he didn't think it was ready yet?
About the 3DS, I think you're right to say it's the culmination of earlier ideas, but Nintendo did probably think it would be the right thing at the right time. Beside 3D not really being a vital part of playing the system's games, that inherently makes it kind of a gimmick. I like it though. I always play with the 3D on, it makes me better at things and infact it made me worse at jumping for example on a regular screen!