Um... I'm not sure if this is what you're looking for, but here's my thought...
I've only used epub until I downloaded the most recent firmware. I decided to try out the CoolReader thing, and see what all the hype was about. So I loaded some .rtf files, and also added a .fb2 to the end of one of my epubs. The main thing I noticed was the little status bar at the top of the screen. When I read epubs with whatever software it normally uses, it's just the text on the screen, much like a paperback. But with the CoolReader, there is a status bar at the top of the screen that shows me the current time (as of the last page refresh), the page number and how many pages remaining, and the title of the book. I really like that, because when I read several books by the same author, sometimes I forget which book I'm reading. So it's nice to just glance at the top of the screen and see the title of the book. Also, when I'm reading, it's nice to be able to see how far into the book I am, and the time. When I'm reading a normal epub, I just press in the little scroll wheel on the side, and at the bottom I can see the time and the page I'm on. But it's nice to not have to press any buttons, and have that information right there.
However, I don't really want to change all of my books to another format, or even add .fb2 as an extension to the end of all my files. So for the most part, I'll just read them as they are, as epubs. It would be nice if CoolReader gave the option to open an epub, without the extra extension.
Also, I'm used to the bookmarks and zoom in epubs, so that's kind of nice. I don't really care what font I'm using. And for the books I've tried, epub had better formatting. I could get good formatting using CoolReader, but I had to play around with it until I got what I was looking for. I don't know if that's just because of that particular book, but I haven't had any trouble with formatting in epub. I like that it's already formatted.
If that's not quite what you're looking for, then hopefully someone else here can be of more help.