Reading the various Kindle forums, I frequently come across people who are using Feedbooks, when they can find the books they want there, because of the formatting. In particular, people seem to prefer the chapter dots that allow you to navigate through the book easily, at least on a Kindle.
I don't have that many books that I've formatted for Mobileread, but when Kovid is able to find time to act on a bug that I've given him a ticket for, I'll go through mine and reformat them.
As it is now, taking a PRC file and converting it to a Mobi file, paragraphs that start with an italicized word don't get indented. This includes any poetry that is italicized. I've recently found that words in bold type react the same way, no idea why. Looking at the books with a text editor doesn't give me a clue as to why Calibre is acting the way it is.