I had to re-set a handful of settings, of course, in particular the nohidden flag so I can see my own goddamn Library folder, honestly what do they think we are fucking two year olds? And, because I do website development, I had to go through the command-line song and dance to re-enable php and re-define /user/Sites as the root folder for the built in instance of Apache, which was exactly as much of a pointless pain in the ass as always but at least no more so. Aside from that, though, this was a remarkably smooth upgrade.
Download of the installer took about ten minutes, and that was only the day after release. Installation itself took about an hour total, and only badgered me for authentication twice, once at the start and once at the end. Nothing crashed afterwards. There weren't even any alarming hang-times.
Of course, I did my homework and updated my Javascript runtime instance beforehand (and even so Vuze was a diva and demanded to update its own local version separately, but that was one of those "hit yes and make tea while you wait for a restart" things, no pain involved). But all my Adobe and similar products lit right up the first time I opened them after upgrade, with no snarls. And I'd already turned off my Calibre notifications, which is currently causing crashes on that one. So everything works and nothing is too weird, though I could do with a few more options for the interface settings of Notes (for which read: any options at all, especially larger font without having to manually select all and increase the font size of every note individually or else edit /Applications/Notes.app/Contents/Resources/en.lproj/DefaultFonts.plist, I mean seriously).
I even quite like the new Calendar, which gives much more sensible views of your schedule at month end-and-start than the old "fake blotter" model.
However.
As I said, I updated mostly to get iBooks on my desktop. And most of iBooks is very well done. The Category (that is, genre) and Collections and Authors all manifest as sidebars from which you can select to see the books in that group, and it's easy to switch back and forth among them. The "shelf" (grid view, rather) discreetly vanishes when you select a book to open unless you click the book's toolbar to get it back, and returns just as automatically when you close the book window. Once you click on the body of the book window itself, the space-bar will page forward/down like any sensible desktop app. There is no page animation, but there is the very briefest instant of slide animation to cue the eyes that a new page has been "turned" to. You can have iBooks display author and title in addition to cover, for each book on the "shelf", which is a definite value-added option. Best of all, you can have more than one book open at a time, a true boon for academics.
Minor gripes: the authors are sorted by first name, not last, which is utterly counterintuitive to me, and you can't change that. The sort options within groups are by title, date-added, or manual, manual meaning literally drag and drop, with no option to sort by author within a genre or collection which is frankly a bit of idiocy. Those are relatively minor, though, and I've certainly seen worse in other reader apps.
There is truly only one unforgivable sin Apple has committed with this app, but it's a doozy: there is no way to access a book's metadata any longer. In iTunes, you could change a book's metadata just like you could change the data of any other file. No longer. If there's a typo in the author's name, or you want to change the category/genre to something more intuitive or useful to you? Tough luck, sucker! There's no way. You can't even hunt down the iBooks folder of book files (which, incidentally, is hidden inside a container so you have to find the container where it's tucked away in a very non-obvious place, right click and tell it to show package contents, and then navigate to the actual book file folder from there) and open the file there to change anything via Get Info, because every book file is renamed with a random alphanumeric string and you can't tell which is which! The intention seems to be to make it as impossible as can be to do anything with the book files except through the GUI, and the GUI has no options for editing any of the metadata. Absolute fail, Apple, absolute fail.
Just to make things even better, just when Apple has figured out how to make Collections and Authors and Categories useful for organization and navigation in the desktop version, the iOS version of iBooks has made them absolutely fucking useless. It used to be that viewing Authors gave you all the authors in your library, and same for Categories. Now? Those views only give you the authors or categories inside whatever Collection you're currently in! Hello, what the fuck good is that going to do me, Apple, you morons? The iOS iBooks has just become nearly un-navigable unless you either a) use only Collections to organize and find things or b) don't use them at all. Can you actually fail any harder on this front, Apple? (Ironically, using the Author 'view' within a collection that you are also viewing in grid/shelf format acts to order the collection by author, the one thing that the desktop version won't do. Are these versions being developed by two mutually feuding dev teams or something?)
So my verdict: use Calibre to curate your ebook collection, and only use iBook to read and annotate it across devices.