Remember that in many ways, the Kobo collections are more powerful than folder based, in that a book can belong to as many collections as you want.
The only missing ability is the ability to have a hierarchy of collections, but as long as you don't mind seeing all collections in the main list, you can end up with a scheme like
- Discworld All books in the Discworld series
- Discworld - Witches Just the books in the Witches sub-series
- Discworld - Death Just the books in the Death sub-series