Best Device for large ebook collections

Hi,

I'm in the market for a new ereader. I'm currently using the original ipad mini (still running iOS 6) with Marvin as my reader app and Calibre on my computer. I have a large collection of ebooks (>1000) that are organized in Calibre into Collections.

I was looking to upgrade to a new ipad mini until I heard that iOS 8.3 bricked the ability of Calibre to connect directly to Marvin. So I'm probably not going to be buying another ipad unless there's a similar reading app to Marvin.

So my question is how are the newer Kindles (like the paperwhite)? I have a Kindle 3, but it was a pain to add books to collections so I didn't use it for very long.

Ultimately, is there any device out there that will communicate with Calibre and transfer large collections of ebooks that will show up in the new E-reader already organized into collections?