I think the thread title is more than a bit overdone!
Like others here, I have both the iBooks and Kindle apps on various devices. Personally, I don't much care which one I'm using to read particular books, so far at least. I am very impressed by the many little touches of elegance of the iBooks application, I must say. It's very, very tough to beat Apple on UI.
Basically I'm used to taking books in whatever shape they're in, including ratty old used copies without their covers from a library's annual 10c sale. So probably I will never do a feature-by-feature comparison of book-reading apps, even though I am thrilled that they exist. If I were doing a research project and so having to focus on bibliography and footnotes all day long, and how to navigate back and forth through multiple books efficiently, probably I would be a more discerning critic. Just reading for the love of reading, either the Kindle app or the iBooks one seems to work for me.
Shopping preference: I'm more used to shopping for ebooks on Amazon so at least for awhile I may still tend to go there without thinking through my options, I guess. Especially since I'm often web browsing when I decide I want to see if there's an ebook version of something mentioned on a site I'm reading. However, I am curious to see more of what's in the iBooks store, so I am trying to remember to prowl around in there even when I'm not looking for a particular item. What I've bought from the iBooks Store so far has downloaded quickly and the whole process seems more or less like buying a movie or music album. I like the option to get a chapter into my ibookshelf first and then buy it later if I want to, just by clicking in the designated place on the freebie.
I usually also have a couple audiobooks I'm listening to. Sometimes I end up flipping through various devices, launching Kindle and iBooks, wondering what the heck I did with some book I was "reading" -- before remembering that it's actually in some iPod's iTunes library and I was listening to it, not reading it. And last week I went looking for a book on my laptop when it's actually the hardcover book that I own, duh.
Maybe I need a vacation from all this technology...