The kindle is monochrome so any colour pics will not be as good. Also, I find reference books
harder to deal with on the kindle as it is difficult to maintain multiple points of interest in the same way - flicking back and forth is trivial with a dead tree book.
Searching is way easier on the kindle though
I also find the kindle less effective than the iPad
for reading PDFs as it is almost always necessary to zoom a PDF to read and the user interface for moving around a zoomed doc is poor compared with the finger flicks on the iPad
For proper ebooks read in a linear fashion I love the kindle.