@alex165, go for a Kobo Libra H2O. It has a 7" screen.
There are advantages to collections. With collections, you can have the same book in multiple collections with only one copy. With directory based organization, you would have to have multiple copies of the same book.
Yes you can install KOReader on a Kobo and use directory based organization. But as I've never used it, I cannot say how the rendering compares to using RMSDK (ADE) that comes with a Kobo.
Everything else can be done with a Kobo without needing KOReader.
I don't know if your Kindle had a cover, but you should have one with the Kobo to help protect it.
If you don't mind an 8" screen, you can get a Kobo Forma that has a plastic backed screen for much less change of the screen breaking.
So there you have it. Kobo will do what you want.
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