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This will only work if you're comfortable with the idea of removing DRM, but my suggestion would be put all the books from every store into Calibre and tag them how you'd like (genre's, etc.), set series info if desired. Then pick out a favorite reading app to use for everything and make sure all books are in the proper format (convert as necessary). Then use Calibre Companion to transfer and catalog the books on your tablet(s). CC will give you great flexibility allowing you to browse by series, author, title and whatever tags you have assigned a book.
Some screen cap examples of CC are attached...
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