I enjoy reading the Kindle version of the S.F. Chronicle, but it is a different experience. The newspaper is usually available by 6 am each day, and this suits my schedule just fine. The Kindle version has a summary page which shows each section of the paper and the number of articles in each section along with a short summary. I can use this page to read just the articles that are of interest to me. The ability to cut and save articles is also a big plus. As some reviews have pointed out, there are no ads, obituaries, sports box scores, movie listings, etc. Some of these omissions detract from the electronic newspaper, and I hope the Chronicle will consider listing, for example, the obituaries in the near future and making other changes.
The main difference for me is the fact that it takes me much longer to read the Kindle version of the Chronicle. I have a tendency to scan through the articles and this isn't possible with the Kindle. Perhaps this is a good thing. Before the Kindle, the Chronicle was always a morning paper for me, but since I carry the Kindle with me, I find myself reading the newspaper at various times during the day.
My overall impression is very positive. The 2nd version of the Kindle provides a very convenient way of reading newspapers, magazines, and books, and I am already looking forward to the 3rd version which will hopefully offer a color screen.