It would be nice if sometime in the near future, Notch changed the 3D Anaglyph to what the new movie/tv shows are using, with the freebie glasses they give out at the theaters. Not use the old system of blue/red that makes you go cross-eyed. I believe this could add another element to the game and make it that much more addictive.
There needs the regular anaglyph red-cyan to be fixed first before stereoscopic 3D. Now it looks as if...it hurts to look at things in anaglyph mode. What you suggested was stereoscopic, not anaglyph.
Update 3D Anaglyph
Poll: Should Minecraft update the 3D anaglyph to use the non red/blue
3D opinion
Should Minecraft update the 3D anaglyph to use the non red/blue - Single Choice