I think the depth could be increased on some of the more 2D type segments (for example, by place the people at screen depth and making the background further back).
Thanks for the very helpful feedback, cyberreality! I think I will try this on the next video I do.
Also, do you know how to use YouTube3D? You shouldn't have any videos in anaglyph format. If you upload in side-by-side, full color, 3D, then people can choose different methods.
Yep, I discovered that halfway through the making of this video, but didn't want to change course. I wrote some custom software for exporting the left and right images out of my animation program and then combining them to an anaglyph movie (and doing other things, like having the ability to alter the convergence from frame to frame). If I put in the time, I could export the result in a side-by-side movie -- and if I end up releasing on Blu-ray, I probably will. For right now, though, I'd rather use my limited free time towards working on the actual content of the videos.
Thanks again for the feedback -- it's greatly appreciated!