Hi Mike,
I've used a few different apps for reading electronics books. I find most of the ebook readers to be about the same from a user experience perspectives. I've used Kobo, iBooks, Kindle, Readmill and Get Abstract (does as the name suggest). So far, my least favorite app is the Kindle. I don't like the fact that all books on the platform are in the proprietary Kindle format. No ePub support at all but Amazon.com does have the largest catalog. iBooks has a smaller catalog but supports the ePub format and, I agree, a great book store design. All the free or self published books that I find on the web cab be downloaded to iBooks.

Readmill is my favorite eBook reading application although it has limited platform support and a possibly a small catalog. The user interface is easy to use and the store is powered by ... many online bookstores except for iBooks and Kindle. I prefer the sliding animation for switching pages instead of that horrible skeumorphic animation of the other reader.

With Readmill, you purchase an ePub or PDF somewhere on the web. Upload any ePubs, PDFs or ACSM files (The ACSM file is the license for the PDF or EPUB book you bought) and they will be automatically synced over to Readmill for iPad.