Lot's of pdf bashing here. PDFs have some nice features. First, it's an open standard ( ISO 32000-1:2008) with free readers & generators on a variety of platforms. That's huge. Second, pdfs are predictable and consistent from device to device. A word processor or html doc will look different from machine to machine. Unfortunately, that consistency means if the pdf is somehow suboptimal for a particular device, it's harder to get optimal output.
For the most part, pdfs are formatted for printing on standard paper sizes. There's no reason they have to be formatted that way. One can just as easily generate Apple Ipad mini-sized pdfs. For example, i've been reading a Japanese pdfs formatted for the Sony Reader. These look pretty nice. (PDF is also the only way to get vertical Japanese text on my reader.)