I just gave up in converting ebooks , you guys know what I mean.
When I use Kindle for iOs I just download or open the book from the original source, which is Amazon and that's it.
Kindle for iOs is mature enough to provide good fonts and basic or simple features like black background and brightness control.
One key feature that I can't compromise is landscape mode on a single page form, not divided in two. This is horrible for technical books. I've found most reading apps out there, including iBooks, divide the screen in two when you're in landscape orientation; that's ok for most books but IT related books.