I think the Nook Glowlight can organize books via directories. You can just drop them in. But check this in the Nook forum. It's a pretty good device, and with the new Nook devices coming out, you might be able to pick the older model up cheap. I think it's a pretty nice device. It does only offer about 500 MB to store side-loaded picks, but that's plenty and you can move stuff on and off.
Kobo is good too, but you will need to install Koreader / Coolreader if you want to organize via directories. But it's perfectly doable. The H2O is nice. But you can't organize books via directories using the out-of-the-box UI called nickel, which is a pity because it's really nice with immense functionality.
Obviously any open Android device will do it and offers the greatest felxibility of any device.
I recommend you don't touch Kindle. The UI and functionality is are super-limited and getting worse all the time. You cannot customize them in any way.
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