It was horribly executed....
The stream was laggy, it kept crashing, and it didn't feel special at all aside from Mario Kart 8 and Smash footage. All they received was backlash and hate for not having a tradition conference, and it hurt them. So you think Nintendo will hold their conference live at E3, or will they repeat history and choose to have yet another conference that will probably have the same problems?
A live conference will help, especially if they reveal big major games, they'll be able to get a live reaction. Like a Starfox or Zelda U trailer.