This is an interesting discussion, thank you. It would be great to see it compared with the parallel ImageMagick methods: http://www.imagemagick.org/Usage/anim_opt/
Also keep in mind that the compression efficiency and quality depends a lot on the content and how you play with the encoding options (how surprising...). I tried to cover most of the cases in my post, but make sure you are "fluent" with the other tools as well to make an objective comparison.
Overall, I think FFmpeg trump-card is that it includes the whole stack; timing, decoding, filtering, encoding, everything is in.