I don't know if there's anything scary about it... it's just that you need an IQ comparable to Albert Einstein in order to understand the encoding guidelines:
http://tasvideos.org/EncodingGuide.html
The complexity of it could be a little scary though. But even if you understand it, it still takes some time/work. If the encoding was easier and faster, using a more automated process, more people would be willing to encode. Just when I read the "requirements" in the guide, I notice I need like 10 different things... couldn't it all be done with one or two encoding software, like avidemux? Or something like Windows Movie Maker, heh... that's easy to work with. To add subtitles, I just click add text, so it's much easier than this:
http://tasvideos.org/EncodingGuide/PreEncoding.html
Edit: noticed that andymac and others already said pretty much the same thing.
Edit2: another problem is that audio gets off sync for long movies when you capture with mupen64, which makes it impossible to make encodes for long movies.