EDIT: I have not yet tried the Retina mini as a Paperwhite replacement except for an hour in the Apple Store. It's on the way. The in-store experience satisfied me sufficiently, but there is a chance I will come across a deal breaker.
Thats 100% subjective, and not having used the new Mini perhaps it really is that good.
iBooks will sync bookmarks and notes for 'sideloaded' epubs and will automatically transfer new books onto the air. For PDFs the kindle app is great because it actually shows the table of contents(!).