It should not surprise you then that I prefer non-DRM ebooks. DRM ties your books to the particular platform you open them first.
The last issue is actually a quite fundamental problem with ebooks, as most of them are copy-protected. Not a nice thought if you rely on your annotations! And most importantly, it locks you into a particular ecosystem: you cannot take the ebooks and their annotations and start using a different system for reading your ebooks (either different software or hardware). Also, there is always a risk that somehow the annotations get lost or detached from the ebook. This makes it harder to read my annotated ebooks on another device. Instead most ebook readers (iBooks or Marvin) store the annotations you make in one local database. My main problem is that, unlike pdf, epub (the ebook document format) cannot store annotations in the ebook itself. But I found annotating ebooks a nuisance. I often add highlights or notes to the digital documents I read.