I was in Pompeii earlier this year. If you really want to go there, make sure to do it first thing in the morning, and find a guide to take you. A 3h walking tour will be enough to give you a feel for the place and you won't be bored. Let me stress again, find a guide, or you'll be walking in circles and hate the experience. Access to the site is easy with the Circumvesuviana, with a train station right in front of the entrance.

Naples deserves to be seen, and I would recommend it over spending the day running around with trains and stuff. I would stick to the city, a pizza or two, and a relaxed day enjoying the views.