Personally, I would suggest a Kobo Clara 2E with the internal 16GB µSD card. This can be easily upgraded to 128gb if 16GB is not enough. This would require adding KOReader to the device.
Unless you want to use KOReader, the default GUI does not have a file manager. OTOH, between the ability to sort and search by title, series, etc. and search being so much faster than trying to use a file manager, I don't miss trying to navigate a directory tree. Even when I use KOReader, I use it's search though that does assume that you are using calibre and it's metadata file stored on the ereader.
Search also removes the issues of dealing with books and series that have multiple authors. Shared universes are one often horrible example. I'm re-reading the Thieves' World books and finding a story written by John Brunner as an example is very simple. Simply type 'joh' in the search box brings up his name and tapping on that brings up a list of all the books where he is listed.
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