Interesting you claim that - I actually put together a rather in-depth report at the time and VP8/H.264 performed very closely as formats (that is, quality metrics vs. filesize were very comparable even if encoding time of x264/libvpx wasn't) and theora was just awful (SSIM and similar quality metrics were behind for like 30-40% which was a lot).

The article you've linked it talking about some decoder implementation details which I'm not sure were all that relevant for end users - x264 was always the superior encoder, libvpx was "ok", libtheora was terrible when it came to actual encoded video results. Not sure what the article you posted really proves around that.

Theora is VP3 with some more leeway in the hope that the encoder can use the additional parameter freedom to produce better video (which never really happened; most of the 1.1 branch was, as I understand it, just cleaning up a lot of old mistakes around e.g. rate control). It's pretty clear that VP8 outperforms it.