I've had every generation of physical Kindle device (yes, even the DX…and I loved it) and have used every iteration of the iOS software, and still, after all of these revisions, I have a single niggle with each implementation (that doesn't exist in the other implementation).
In iOS I hate that I still can't scroll through my books. I’m instead made to page through them like it's Q12006. For whatever reason, and it may be just a feeling, I feel like I read faster when I scroll. (Maybe because I tend to keep my eyes focused on the same physical area of the device and scroll content through that area?)
With the physical devices, the thing that still really irks me is that it insists on showing the percentage of the book completed. I was hoping the Voyage would rectify this, but no dice. Amazon, no one wants to see this all of the time! You've always hidden this in the iOS app, so why not here too? You hide it in the web reader as well, and the Mac app! (UPDATE: Minutes after posting this, David Dixon reached out to me on Twitter to let me know that this information can indeed be suppressed on the physical devices. On my Voyage, I simply tap the bottom left of the screen, where by default it says “Loc XXX”; tapping there cycles through the display options, including displaying nothing!)
All of that said, I LOVE my Kindle(s), and continue to read like a crazy person.