The advantage of using the app store micropayments is that users don't have to create a new account somewhere and put their account info in your app. They can use an existing system and have a one-click buy option.

It'd be interesting to see what will result in more profits. My guess would be that the increased sales on the iPhone outweigh the higher profit margin with the alternatives. This depends on your costs too of course (e.g. copyright fees for eBooks)