Honestly, I liked how the Nook Touch/Glow handled PDF files considerably better. For textbooks, especially. It would pull the text out and reflow it so that you could change the font size to fit your needs, and then just read.
The Kindle only allows you to zoom in and out on a page-by-page basis, which means you need to constantly zoom and pan.
My textbooks, however, are full-size. Maybe if yours are not, you will not find this to be such an inconvenience.