Hmm, I tried the above suggestion, but actually got worse results. Theoraenc produces much larger files (essentially not hitting the bitrate), so you have to keep that in mind. I suspect I have to do something additional to get theoraenc to use the most recent libtheora on my machine.
Anyway, it seems unlikely that theoraenc is going to get much better results than ffmpeg2theora if they are calling the same underlying library. On the other hand, I can certainly imagine some flag or other that would optimize the encoding better. My preference is to use ffmpeg2theora for the web examples, since it is the most commonly referenced tool on the web for normal people to do Theora encoding. If there is some way of getting higher quality encodings ... well it seems like ffmpeg2theora is going to support it.