What's wrong with Joshua Allen's coment on yEnc? One simple thing: yEnc tried to solve a problem in a way that is not stable: there are already implemented standards for encoding, but yEnc ignores them all and put's it's own on top of NNTP and Netnews. It ignores all RFCs in existance and reinvents the wheel.
Will this break things? Sure, it already did. Not everybody jumps on the bandwagon to implement yEnc, so people have to use external tools to get at the stuff they want. But since yEnc is implemented in the worst way possible, this won't always work. Take for example a bi-charset-Environment like the Mac OS. You usually use Mac charsets externally, but talk latin1 or other standard charsets on protocol level. So your data get's converted from one charset to the other. Since yEnc doesn't give applications not knowing about yEnc any clue about it's existence, the stuff get's broken.
yEnc makes almost all errors UUENCODE made, but adds several layers of it's own errors on top of it. This is just plain stupid. And that it "works" is no reason - it works to the extent that people using yEnc capable programs can exchange information. But the basic idea of the Internet is to enable as much people to use something as possible. That's why MIME is so complicated, it's idea is to set up markers in adavance to allow programs to know that something problematic is ahead, even if they don't know what it actually is - and hand it over to a helper application.
yEncs stupid idea of body-tags makes this automatic forward-compatible way of handling stuff problematic.
A very good discussion of the problems of yenc is at http://www.exit109.com/~jeremy/news/yenc.html - read it, understand it and you know what is wrong with Johns little talk.