I'm all in favour of preserving the director's vision etc. and have no problem with movies shown in letterbox on 16:9 screens (apart from those people who shoot TV material (Utopia etc.) in letterbox: they should be beaten with a stick) but when it comes to 3D it's different.
The best 3D, in the movies I have, is in those which fill the 16:9 screen, e.g. Avatar, Creature from the Black Lagoon or are 4:3.
The vast majority of modern 3D movies are in letterbox and as a result, the 3D effect is diminished.
Zooming in (assuming it's possible) negates the 3D completely.
Surely it's possible to reformat 3D Blu-Rays to 16:9 without causing rioting in the streets.