Its certainly an interesting discussion. Should a feature such as AutoLinking be acceptable where it takes the content that someone wrote and modifies it before presentation to the end-consumer – often in subtle and non-obvious ways.
The discussion is interesting because I fall into both categories – publisher and reader. As a publisher I would like to think that my content got to the reader as I intended without the fundamental structure being altered (links are fundamental to the structure of the web). Typically there isn’t any commercial imperative there – just an artistic whim.
As a reader tools that allow me to get more information are incredibly useful, it’d be great to be able to click on a link and have my user agent suggest some alternative content – although I wouldn’t necessarily want it to obscure the underlying link (I’m thinking some kinda of async data mining panel off to the side).
Where do you sit? Have you considered both sides?