My only real complaint with KOReader is that the book browsing UI is file and folder based by default, while virtually all other ebook readers support some kind of cover based library view you can sort 20 different ways based on metadata rather than filenames etc.
It's not a huge issue, but I find just browsing my collection to find a read a lot more enjoyable on other ebook readers. IIRC there are plugins to add this feature, but it's not present out of the box.
On the few Kobos and jailbroken Kindles I've used it on, it also drains the battery significantly faster than the stock reader app, although not enough that I couldn't last at least a few days. On stock software I can go weeks between charges.