I've read several novels in Amazon Kindle format (on an actual Kindle device, the PC client, or an iPad), and the experience is pretty good. But having now finished reading a technical book that way, I think it's not quite there yet.

The book I read is Jez Humble and David Farley's Continuous Delivery: Reliable Software Releases through Build, Test, and Deployment Automation. I'm not sure if the weaknesses are due to Amazon's ebook platform, this particular title, or some combination of both, but these were the issues I had:

1. The table of contents as displayed by the PC reader application, isn't detailed enough.  The book is divided into three sections, and the sections appear in the ToC, but none of the chapters in the sections do. One of the entries in the ToC is the Contents as it appears in the book itself (which is also where you go if you choose Table of Contents from the iPad menu). It has links to everywhere, but is extremely detailed and spans 19 pages, making it cumbersome to use. There's no easy way to just jump to a particular chapter.
2. Cross references don't tell where they're going in a meaningful way. They reference other parts of the book by page number, but Kindle books don't have page numbers. There is a link, so not all is lost, but I couldn't tell if a cross reference was to some part of the book I had already read (and that I ought to therefore nod and say, "Oh, yeah") or somewhere later on. Maybe just a little arrow icon pointing left or right would have been a good hint.
3. The index is cumbersome. There aren't any links to jump to the different letter sections, so if you want to look up "Tests", be prepared to flip through a lot of pages to get to the T's.
4. The figures are too low-res. One in particular, 15.1, was almost completely unreadable. It sounded like a really interesting chart, but it was just too small and couldn't be zoomed so I feel kind of cheated out of that.
5. Compound words were problematic because the dashes were usually dropped and the words mashed together. Apparently someone/something confused them  with dashes as a result of layout (to split words across lines) and dropped them all.

There's sometimes talk about e-book prices needing to be lower than the print equivalent since there isn't a physical object that needs to be created and distributed. In cases like this, though, it may just be an inferior product that makes it worth less.