I already had Marvin installed, and I reinstalled BlueFire, and I went through the appstore and looked at other epub readers.
BlueFire was still twitchy, and didn't have a way to categorise books. iBooks had a way of categorising and separating books that I liked. I read a book in BlueFire and it's nice, it's got a good display of fonts and yes, it looks really good. But no way to categorise that I could see.
None of the other readers looked interesting. I read a book with Marvin. Not as clean a display as iBooks or BlueFire, but it had a cheerful feel to it. I know that's not scientific, but the display was good enough, the options are terrific, the more I used it the more options I found. Even Dropbox. And a Calibre plugin. And it has a way of categorising books and doing bulk operations on books. I loaded up some of my library and it took it all. I flicked between BlueFire and Marvin, and finally the convenience of Marvin won me. I deleted BlueFire and I deleted iBooks. Marvin is the way forward for me, for the time being.
I just hope they don't do what most apps do - improve them to the point of unusability.
I would have been happy with iBooks. If I had managed my library in the One True Sanctioned Way through iTunes, I would not have had the problem. But I manage my library without iTunes. I hate iTunes. It's a spreadsheet abomination that I use as infrequently as possible. So if a full encrypted backup of my iPad means that iBooks will shed all unsanctioned books, I either have to not back up (not an option), or use another ereader. I choose the other ereader. Marvin.