Amazon has clearly decided to turn their iPad app into a textbook platform. The Kindle iPad app now supports Amazon's PDF format, Kindle Print Replica. Amazon launched this format about 4 months ago as a way attracting publishers who need complex formatting in their ebooks. At this point it's entirely concentrated among textbooks and academic titles, which is why I think of it as a textbook platform.
BTW, I checked and the iPad app can use all the usual annotation tools with the KPR files. You can bookmark, highlight, type notes, and share one of these ebooks just like you can with other Kindle ebooks. The app also supports the external TOC used by some PDFs and it has a nice interface for browsing. Click on the lead photo for an example (it's from the iPhone app).
Now, the iPhone app didn't get those 2 really cool features, but it did get a lot more useful today. Both the iPad and iPhone apps now support PDFs and they got a new library layout. You can now choose to see just the ebooks bought from Amazon, personal docs, or periodicals. And both versions of the apps now support for the Kindle Cloud.
The apps can also download the personal ebooks that Amazon stores for you in the Kindle Cloud, the 5GB of online storage that all Kindle owners have. They don't have their own email addresses, but you can send files to your general Kindle email address and then download them from inside the app.
I was hoping for the direct email support, but this is almost as good.
All in all, this is a major update. Go get it now.