I'm looking for an ereader, and, if I am not mistaken, my objectives are similar to yours.
First a disclaimer: I don't currently own a tablet / ereader.
It sounds like eye comfort and clarity/contrast are probably important to you. If so, then I think e-ink is the best idea. If you want something not too expensive, NOW, with e-ink, that displays pdfs, including scanned pdfs, acceptably well, then the Kindle DX is perhaps the only choice. Others are smaller or more expensive. I am not sure about annotating in the Kindle DX - I think that might not work

That's one reason that I'm waiting. I am pretty sure I want something with e-ink. I am quite often at a computer, and I have a web-enabled smartphone, so I can read my RSS feeds and browse the web almost as much as I want. The slight inconvenience of not being able to get live updates of my blogs on my ereader would not be a big deal, especially considering that I don't plan to pay for another 3G plan or other 3G data service (I don't live in the US). The actual act of viewing text on a surface with my eyes, in comfort and with high efficiency and portability, is my primary concern. So, I don't really want a glossy screen. Other concerns are note-taking and portability. I would love to be able to write into my ereader - the PocketBook 902 will have stylus input. Also, the PocketBook 902 will be 3XX grams and will have a plastic non-glare screen. Unfortunately it will be out sometime around September or November! (The PocketBook 901 will also be out around the same time, and not include stylus input.) Finger touch-screen input doesn't make much difference to me.
If you are considering a tablet with LCD, and you can wait, then I think you should consider the Notion Ink Adam, with Pixel Qi technology (which should be nicer on the eyes than other types of LCDs). I do think that the ipad has a nice interface, but the Notion Ink Adam is probably going to be a better value, considering that it will have a Pixel Qi display, will run Android, and will be able to run a variety of Android apps, sort of like the ipad can run iphone apps. I might be biased, since I develop Android apps, but I am pretty sure that Android will have enough apps. The other thing is that Android is more versatile in some aspects, such as multi-tasking. (iPhone / iPad will allow a limited form of multi-tasking fairly soon, but Android has multi-tasking now and the multi-tasking works in a broader range of apps than the planned iPhone / iPad multi-tasking.)
There is also the
Entourage Edge, but it seems like the e-ink display is sort of low quality (only 8 gray-scale levels?).