If you have trouble with the default software on a Kobo ereader, you can install other applications aside it, then switch to them after boot. In my experience, the installation process is innocuous and straightforward.

I use Koreader: after experimenting with various configuration parameters for a few days, the UI is now stable and tailored to my taste. Once in a while, I switch to another app: Plato is better at handling huge PDF files.

Another bonus point is that I can mount my ereader as a USB mass-storage and rsync the git repository of my ebooks onto it.