Honestly, I don't like Freeport and look at it as a bonus day on the ship (I prefer the ship). In Nassau going over to Atlantis is worthwhile, although you need to watch the prices. It is most definitely not a cheap place.
What do you like or want to do? Are you water people? Just want to driver around and see the sites? I recommend doing a dolphin swim at Nassau but that isn't everyone's cup of tea.