KOReader, in comparison to Amazon's native Kindle operating system, offers more features for PDF documents. However, KOReader's software is not stable and the interface is convoluted. The KOReader project is an excellent community-driven project but there has been no stable release since November 2015. Thus, to get the right version to work with recent devices, e.g., the Kobo Aura One, it is necessary to download and install a nightly build.
Despite the extra features that KOReader supports, I still prefer Kindle's software. In my opinion, what makes the Kindle's software preferable is its simplicity. The menus are simple and clear - there is one display settings menu that changes orientation, margins and increases contrast. The pinch to zoom, relative to other E-Ink e-readers, works well. Further, highlighting is smooth and dictionary, Wikipedia and translation look-up are all supported. In other words, Amazon put some thought into their PDF support and get the necessary features right.