I've set to see a reason for leaving it out that doesn't suck. The animations for certain things take like half a second longer? Oh no, what a horrible loss.
So yeah, I want them back, but I guess a way to disable it would be good too, just so you can please everyone. --- If you think Majora's Mask was one of the best Zelda games and would like to see a 3D rerelease, go here: http://petitiononline.com/MajoraM