I have provided them to Sergio before. I'll try to distill.
1. Table of contents is separated in two panes on both sides of the main content. I think this is a harmful decision. The main content is just a single narrow column of text. This narrow column forces to split text into shorter and shorter paragraphs to remain readable, until each sentence ends up on its own paragraph. This is a booklet/brochure format. I don't think this is the right format for a book, as we are not trying to grab attention here. Design should disappear and let user do his stuff.
2. Table of contents should appear at one place - left-hand or at the top. It's really strange that you click on a topic in the left pane, and then an update happens on the right pane all the way across the main text, but the context for both panes is the same - providing user with a ToC. Also, the right pane is called "Table of Contents" but it's ToC for the current chapter only, not for the entire book. Then you have "Book chapters" on the left - is this the full ToC? (Should "chapters" be capitalized?) I very much prefer the old system with just one ToC at the beginning of the book, as in all the books we read, or ToCs appearing at the beginning of the chapters.
3. I don't like complex CSS getting involved at all. The less CSS/JS, the better. I appreciated Handbook being a simple HTML. I hate when web pages begin to hide elements, or things begin to slide, fold and unfold, text moving on the screen, and so on. I am here to read the book, learn things and do my stuff in the other window. I would do everything as static as possible. The less the UI interferes with the reading process, the better. This includes the two ToC panes that are scrollable. It's like reading a book with inserts.
4. Do we really need the "top" button at the bottom of the page? Why would want to clutter our screen with that button if there's a Home button on the keyboard? Are you optimizing for tablets and phones? But most mobile devices can scroll back to the top, at least iOS can. We don't need another element here.
5. Interline spacing is not for a book - too much space between lines. Is that 1.15 or 1.2? I'd go back to the old format.
6. The font is gray - we are loosing contrast and straining eyes for no good reason.
7. The font system doesn't match FreeBSD's web site. Is there a FreeBSD style book?
8. The hyperlinks are not underlined and are now more difficult to find and identify visually.
9. There should be vertical indent between paragraphs.
10. Random irrelevant italics. Quick example: paragraph 2.2. Architectures are in bold italics. I can understand bold here, but why italics? Although I'd make bold a little less pronounced. It really screams a headline where it shouldn't.
11. The code snippet background color, e.g. paragraph 4.3.1. It was a pleasant almond in the old book. Now the background is black. We are inverting from grey text on white all the way to white text on black. This strains eyes. I guess this was a simulation of a terminal window, but not all terminals are black. This inversion breaks the coherence IMHO.
12. Chapter/section/subseciton titles were dark red in the old book, which helped to "unglue" different subjects vertically, especially in a single HTML. Now they're all grey. There's a barely visible (actually to the point of irritation!) horizontal underlining in chapter titles, but as it's an underline it actually contributes to the vertical clutter.
13. Filenames were green in the old book, and now they are grey, but not only that - they're extremely bold. This one is controversial, but I really dislike jumping to that much bold in the main content - I think it interferes with attention and makes the text look incoherent, as bolded out filenames stand out from the rest of the text. With that much bold, and especially with main text being a subtle grey, filenames really grab too much attention and even compete with chapter titles.
14. Warning and note section titles are in the serif font. Why suddenly serif here - what is the reason? Don't get me wrong, I really like serif. I would switch FreeBSD all the way back to serif, I think it was pleasant for the eyes and easy to read.