I like to take notes, too - at least when I'm reading something 'serious', something worth giving extra thought - and taking notes helps me remember and think.
Making notes directly in the book has never worked for me though. There's never enough room, I can't write tidyly enough, and the paper is often not that nice to to write on (wrong texture) - and I just don't like to mess up my books with writing
So I've always made notes on separate paper.
Because of this, the Kindle is close to perfect when it comes to note taking - and not having the large hands that a man might have, the keyboard is really great, and I definitely prefer it over a virtual keyboard + stylus.
Perhaps if I'm proof-reading it might be nicer to make freehand notes with a stylus, but highlighting works well, too.