I haven't used Aldiko. However, there is one thing you might want to check and compare.
FBReader loads the whole book into memory when you start the app or choose a book. This means that it takes a little longer to get into your book but the scrolling/paging is then seamless as it has already been loaded, parsed, etc.
I like this as slow scrolling annoys the crap out of me. Check and compare against Aldiko - though for all I know Aldiko not only has the better/prettier UI but also really fast, smooth scrolling/paging.