[holymadness]

I don't own an iPad mini so I can't answer your hardware questions, but I can answer some of your software questions.

1. iBooks is not bad, though it's not my reading application of choice. It's distinguished principally by its desire to imitate a real book. Hence, book titles and page numbers are persistently displayed on the screen when you read and page turn animations imitate those of real books. You can also choose to read your books as an endless scroll rather than turning the page. It integrates with iTunes, which has its own book section.

2. iBooks reads epub files. It can read any sideloaded epub file whose DRM has been removed. You can easily accomplish this using Calibre and Apprentice Alf's DRM removal tools on your Sony and B&N purchases. Calibre has a function to automatically sync its library with iTunes, or you can drag and drop selected books from your folders to iTunes.

3. iBooks is not installed by default, but it is free in the app store. There are tons of other reading apps available, including Sony, Kindle, and many that are not affiliated with a store or a company. You cannot start a book in one app and finish it in another, but you can easily sideload your files to your app of preference using iTunes. NOTE: the Kindle app uses .mobi files instead of .epubs, so you will have to convert them using Calibre beforehand.

4. Notes are easy to take in iBooks. However, they do NOT synchronize with your computer. They stay in the book and can only be synchronized with other Apple phones or tablets using the same Apple ID. As far as I know, it is impossible to extract your iBooks notes as a text file, or to even view them on a mac or PC. It is possible that third-party ebook readers allow you to do this, but I'm afraid I don't know of any.

5. Yes, all iPads can be wirelessly synchronized with iTunes.