[democrite]

While I can understand the margin choices of iBooks – horizontal on larger devices is an attempt to set an optional line length for readability, and vertical allows the toolbars to always remain open and not obscure text though they are a bit big on an iPad Mini – I do wish there was a bit of adjustment, and that Apple would give a little more attention to iBooks which doesn't seem to get new features very often, for example iTunes and iOS Music mangement for larger collections has had many changes over the years yet iBooks none and font choice, particularly if you want greater Unicode coverage in a beautiful and readable font, still needs work. Vertical scrolling mode is an option if you're ok with it.

For other ePub-only choices, there's Marvin as mentioned (I believe PDF support planned), Hyphen, and Bluefire. There's also Kybook but the design is also a bit dated. Besides that, I can't think of anything else that's modern looking or somewhat modern unless you also want to try Google Books, Kobo, or Nook. As far as the 3rd party indie apps, the ones above I believe most have some issue with ePub rendering. Those that provide adjustments for paragraph margins and paragraph indents, they all have problems with it, each in their own particular way. It's possible if your ePubs consist of average paragraphs without quotes, epigraphs, poetry, hanging indents, etc., you might not notice. I've mentioned it. Let's hope it gets fixed soon. The older Marvin, version 2 now named Classic, works well though still has minor rendering issues. There are other apps, and if you search the store for ePub, you'll find 'em. I've tried some, and others I haven't in a while. None of them that I can remember get mentioned often here so maybe they aren't too notable.

If you want PDF support with highlighting that's fairly easy to sync back to your desktop, a separate PDF app is likely best. GoodReader is a favorite of many though I don't like the UI very much, though apparently it's going to be changed someday. PDF Expert is pretty nice; there are quite a few others but that's what I stick with.