I do agree with Harry. An iPad with GoodReader is the best option.
I faced same dilemma a year ago. I used to have a Kindle DXG, which is eink and big screen. It was too slow for PDFs and lacked of important features like annotations, TOC, etc. It was just to painful to use, especially with technical documents where you need to jump from back to forward without any logical order.
So I bought an iPad 2, paid for GoodReader and can't be happier.
I was reluctant at the beginning, as I'm a DBA and spend the whole day in front of a computer screen, actually two monitors, lol ... but I must admit that during a 30 to 60 min reading session, my eyes are perfectly fine. I do not read longer than that because my MS-SQL is technical stuff, so I need to practice what I read or read it one more time to assimilate. So no matter what, spending more than one hour on a computer book is kind of useless to me.
The iPad 2 is heavier than the Kindle DXG but light enough for using for an hour or less. As a matter of fact, is way less heavy than several of my 1k pages MS-SQL books or manuals.
The GoodReader app lets me add notes, highlight, create TOC and much more just touching the screen and without using painful and slow menus. And changing pages is as fast as swapping or moving my finger on the screen.
For long reading sessions though, like crime, novels (based on IT or computer books, like Kevin Mitnick stuff) or self help books I prefer my Kindle Touch.