It would indeed be great to have a lot more control within the reader app! Several reading apps written a decade ago for PDA OSes had much more flexibility as far as settings and fonts than does the typical reader app for a Kindle, Sony Reader, Nook, et cetera. Sad, but true.

One thing we should mention too is that each ePub has a unique CSS (cascading style sheet) that sets the book's formatting. Depending on how the CSS was written, you might encounter certain difficulties in modifying the ePub via calibre. Generally speaking, the less formatting that is hardcoded the better, but I've encountered a few ePubs that were so horribly formatted that calibre really didn't do a good job converting them and I had to edit the CSS file and/or HTML file(s) to get them to look good. Most of the time calibre will do a good job, but occasionally you will encounter a book that just won't cooperate!