If you have Pages on your desktop Mac, you can open a Word file and export it directly to the ePub format, then move the file to your iPad. You don't need to go to HTML first.

I've been researching how to access the notes I make in iBooks too, and supposedly if you right-click on the book in iTunes and then choose "Show in Finder" a window will open for its location. Theoretically, you should be able to open the ePub file in Page on your desktop, but I haven't tested this yet myself. Hopefully, notes are saved in this file too.

While I agree that the lack of exporting annotations is a pretty big oversight on Apple's part, keep in mind that the software is version 1.0 and is only 6 months old.