OneNote on my Surface Pro is about the best thing I've found, and yet it still has major flaws (this is without even getting into how bad its pdf import is). Capacitive touch + active-digitizer stylus can solve a lot of the problems with ebooks (and indeed does, particularly as far as annotation is concerned), but the software is still severely lacking.

The main UX challenge that I haven't found anything has really solved yet is the ability to show 2 or more pages at once (and do so in a way that's simple & intuitive). Also related is some way to mimic the ability to, with a textbook, stick a pen or finger in between two pages as a "temporary bookmark", to make it easy to flip back & forth.

Now that the hardware has caught up to where it needs to be, I think e-textbooks have the potential to get a lot better as software improves. I don't think the physical book will ever die, but I do suspect that ebooks will be much more prevalent in 10 years than they are now, when the software has finally solved UX challenges like these.