I love my Kindle, it's probably one of the first things I would bring to a deserted island, but there are two things I love about paper (or dead-tree edition, I once read it and found it hilarious).
#1 I can have many books, each lying around in a different room, ready for a quick read. It makes a frictionless serendipity reading just happen, I purposely leave books on tables, in the bathroom, on the balcony, etc.
#2 I can put notes with a pencil, make drawings, and mark sections in a very free-form way. I don't like to just highlight, I like to mark with different intents, e.g., this passage is interesting, this was an aha moment, this was something that I disagree with, etc. I use different symbols for these. I'm not super consistent, nor do I care too much about it, it's just something I end up doing when I have a pencil.