Right now, I think it's obvious that AMAZON has a much better selection. However, I think iBOOKS is the overall better application. If I have a choice - and the prices are the same - I will buy it on iBOOKS because it's my preference. For titles that iBooks does not have, I have no hesitation buying them from Amazon. I've never been into buying e-books before the iPad, so I haven't bought into either system yet. For someone who a history of Amazon books, then the Kindle app probably makes the most sense. And there's a good point to be made in that the Kindle app is on multiple platforms.
Right now, the iBooks app has several advantages:
- In-app bookstore. You do not need to go to Safari to buy books from iBooks. I don't know if Apple permits it or not, but it would be nice if you could do the same from the Kindle app.
- The iBooks app has a built-in dictionary, which may or may not be important depending on the type of books you read. For technical books, it is indispensable. For novels and children's book, probably not needed. ;-)
- I think the iBooks app has better readability in terms of font rendering. And I like the way it changes pages better. I know you can enable the animated page turns on the Kindle app, but it's pretty choppy, whereas the iBooks turning is smooth.
EDIT: Actually discovered the Kindle has in-app brightness control as well. My bad.