1. I already have an ebook library in Calibre that I access on other devices, the sync feature allows me to seamlessly integrate into my other devices.
2. It's highly customization, almost every aspect of how books are displayed is able to be modified.
3. Progress can be synced across many devices without having to rely on some proprietary provider like Kindle.
4. Along with #3, you can get KOReader on many platforms to have the same experience anywhere (Android, Desktop, E-Reader). If I wanted I could push progress from my e-reader and then continue on my phone.
5. Easy shell access allows hacking and general tomfoolery. I don't use this much, but having this available makes me happy.
I could probably list more, but I'd need to refresh my memory on the core software (I've been using KOReader so long I've forgotten much of the original kobo interace).
Edit: Some relevant info in this comment https://news.ycombinator.com/item?id=39999476