Kobos[1] and Pocketbooks[2] are a lot more open than Kindles. AFAIK you can transfer .epub files into both devices and these epubs are perfectly readable via the stock OS. If for some reason you find the stock proprietary OS lacking, you can install an open source one like KOreader[3] or Plato[4]
Of course you want a good way of organizing epubs pdfs mobi, and like has already been mentioned Calibre[5] is a great option.