A bit off topic perhaps, but one bit of feedback to anyone thinking of publishing web-only books: I have yet to read my first web-based book from start to finish.
I find it horrifying to not be able to have any immediate way of knowing where I am in the book (which you have in both e-readers and physical books) and being able to keep a list of the books I'm currently reading, not to mention the abilities to highlight and add notes.
There's been some good writing on the general failure of "Hypertext books" (e.g. the first couple of paragraphs here [0]). I personally think this stems from some of the reasons that underlie some of those that you outline - books published on the web simultaneously try to be skeuomorphic in retaining the physical book metaphor (organized linearly, mostly static and plain text, etc), while still losing some of the real-world effects of the physical medium (being able to intuitively understand progress, markup, etc). The way that we publish and read text actually hasn't changed much, even though the target medium has of course changed dramatically, and as a result you end up with arguably the worst of both worlds. E-readers try to side step the problem by extending the book metaphor even further, but text on the web doesn't have that privilege.
I'm working on a product, Literal [1], that aims to solve some of your specific problems, specifically providing for a way to annotate and add notes to web content and enabling some degree of source management. My ambition is to move on to solve some of the other problems you raise as well. If you have an Android device and are interested in trying it out, I'd love to connect!
I find it horrifying to not be able to have any immediate way of knowing where I am in the book (which you have in both e-readers and physical books) and being able to keep a list of the books I'm currently reading, not to mention the abilities to highlight and add notes.