We will be in Italy in Oct and want to visit Pompeii, Rome, and CT. Should we fly into Rome and go both directions OR fly into Naples and leave from Milan?
Good question and no easy answer: you have to price it both ways, allowing for the savings in time and cost not to have to back track to Rome.
Since it's October, I would start in the north and end up in the south. That way the odds are that you would get the best weather. But if you're only there a week or so it doesn't make any difference.
Try to avoid doubling back.