Although I've never tried a Kindle, there are a couple of features that would make me happier about it. I'm a physics PhD student, so I read a lot of scientific papers, mostly in pdf. It would be more confortable for me to have direct pdf support. Moreover, I love the pen support of iRex or Samsung Papyrus (the latter was announced a month ago, see
https://www.mobileread.com/forums/showthread.php?t=35975 ). It would enable me to take notes over the papers (it needn't be "fast and perfect note taking", just a working feature, as could be seen in the Samsung papyrus presentation), and of course, by mean of the pen you could get rid of the keyboard of the kindle, and bring a fancier, smaller and lighter device.
So, on the whole:
- PDF native support
- Integrated wacom tablet or similar technology, to take notes
Hope it helps