I doubt Kobo will go the Amazon root, though you can currently downgrade your devices firmware to the version it was released with, you just have to download the firmware files, there's a handy post
here with links to many of them (I believe all the current devices and various firmware versions).
I find using Calibre is the best method, using the method detailed
here really makes it easy. I've set up Collections as Kobo calls them for genres, and for the series.
Kobo doesn't navigate by folders, though you could install KOreader which does. Personally I found the built in reader to work very well.