Obviously the short answer is 'it depends', but that's highly unsatisfying. More specifically there are interactivity options that iBooks Author can provide that suit particular books. Children's books spring to mind:
For some authors, specifically those creating highly-interactive titles, their choice hasn't really been about Amazon-or-iBooks, since standard EPUB represents a fairly static output technology. Their decision is more about choosing between an iBooks Author ebook versus a custom, standalone iPad app. I have encountered book creators who have gone in both directions.
There's some great breakdown of strategies and examples in here, including a company that decided they needed more interactivity than iBooks Author could offer:
"We do books as applications," he explained, "Because, frankly, there's no platform that's mature enough yet to support the kind of interaction we create. If iBooks Author could produce the level of what we wanted it to do, we'd use it in a heartbeat. The problem is that it can't handle the demands we put on an interactive book."
If you are working on a title that would benefit from interactivity, check it out here: http://www.tuaw.com/2012/06/17/ibook-lessons-so-what-exactly-is-ibooks-author-for-then/