I absolutely hate any format that is not a pdf file. It puts way too much limitation on the content. Just as an example: I use three "systems" most of the time, one windows, one ubuntu, one android tablet. Pdf works with each one out of the box, I can hight text or copy/past it, edit them, heck even open them in some graphic editing software and extract illustrations as vectors, save it in different formats. In contrast to that, for epub/mobi I don't even know what their native editing tool is so I can convert them into pdfs.
eBooks aren't perfect for everything, though. I think a design book, for instance, is something I'd rather read as a paper book.
As others have said - the issue with PDF's is that they assume A4/Letter size. When you're reading on a smaller screen (especially a basic e-ink one) the content is much more important.