Time has passed since 2009.
Today eink-based devices do good for your eyes, just as good as paper.
PDFs are a terrible format for viewing on small screens, that's why you actually need a reflowable ebook format like epub3 with a device that supports it (epub2 is more supported today wastly, but that's reflowable too).
That said, a modern eink-based ebook reader device will try to salvage your pdf usage with something called "pdf reflow" (which are just random tricks actually, but often effective), or "pdf columns" (same remark).
For example, an ebook-reader like Kobo Aura HD improves on pdf navigation by a mini-map, and has the tricks mentioned above.
For annotations, these are best kept on your private device what is always near you anyway (as it is the "screen"). Just like a real book! For example, my Kindle v3 does annotations. Check other readers, most should too! I use them all the time.
Talking about screens: except it's not glowing, so it keep your eyes calm! This is very important. I can't stand reading anything on lcd. I think it's a terrible idea too. Einks are cool for your eyes (in a good sense).
That said, physical books still have advantages not repeated anywhere in the digital world, and particularly unsolved on eink devices:
- physicals being a "clarity of overview" - visually, and, damn, physically!
- physicals are the "natural existence" of navigaiton. I call it "more than intuitive" because it is what it is. Your brain expects real-world points and qualities for navigation, like weight and breadth - physical books are that, devices cannot be that (something needs to be invented instead).
- physicals are annotated freely and instantly, effortlessly, joyously. devices suck (but does some of the job).
It must be noted that there is a great difference between reading on lcd and eink. Einks are like real books, you can read them all day. Lcds will tire your eye just as anything you do on monitors. Remember crts? What crts were to lcds - that kind of difference.
The eink devices you keep always around, and they have a usual uptime of weeks to month.
My personal advice that don't try to use the eink ebook reader for something else, ie. don't try to make a tabletpc out of it. Treat it like it were a book. That's because while these devices struggle to be a competition to tablets, it's just an effort in vain because wifi kills uptime for example. Also check carefully for pdf capabilities, international support, annotation, and maybe folder support. Try to test it before you buy it at any cost if you have the chance (eg. we have this CES-like day events for ebooks what tries to popularize them, or just walk in a shop that sells them if you could.)