We've done a couple of nights in Miami, followed by the Key West / Bahamas cruise on Majesty of the Seas. It was fab, you'll have a great time.
Favourite things in Miami were jogging along South Beach at sunrise (jet lag !), walking along the Art Deco district, people watching in Lincoln Mall, and the Thriller power boat ride out of Bayside (cheesy but a bit Miami Vice !).
Loved Key West, don't miss the Little White House, and Earnest Hemingways house, plus a walk to the Southernmost point of the USA. Also Key Lime pie at Kermits.
The trip to Atlantis was good, your teens would probably love it, but it's very expensive to book an organised tour with Royal Caribbean. I think you can do it cheaper by getting passes to the aquapark by booking a day room at a nearby hotel ( i forget which one), but check out Cruise Critic, there will be lots of information on there.
Another good trip there is Swimming with Dolphins, that was amazing.
Coco Cay, if you are stopping there, is a great beach day, very busy in the main area of the beach, but if you walk on round along the beach for a bit, it gets much quieter, and prettier.
Coming back into Miami, we had an evening flight home, but docked very early in the morning. We booked a tour with RC to the Everglades, fairly expensive for what it was, but it was furn, meant that the suitcases were looked after, and we were dropped at the airport by lunchtime. From there we caught a shuttle bus to the Dolphin Mall, had lunch there, and did a bit of window shopping. Couldn't buy much as our suitcases were already checked in, but it was a nice way to spend the final few hours rather than hanging about the airport.
Sorry for the essay, hope it might give you some ideas. Enjoy the trip, i'd love to go back !