1) are you a first time cruiser? I might suggest a 5 night is long enough to see most things, but shorter in case you find you don't care for cruising. not all people do. 3 day is definitely too short for a first time cruise, you will spend that much time figuring things out, not relaxing.
2) As has been mentioned, the conventional wisdom is the boat rocks less in lower levels mid ship. If you know you dont get sea sick you can think of some of those higher levels and bow. aft some people complain about engine vibration.
3) however, when choosing a room look at what is above or below you, you don't want to be right under the deck chairs for example, can get noisy. its like not choosing a room by the elevator in 3d
4) if you are going to
castaway cay, get a cabin on the starboard side for the best view
5) do get a verandah if you can.
6) I tend to avoid rooms right next to the larger suites as those tend to have children. yes I over think things.
7) choice of ships is really a personnel thing, there are good things to be said about them all. some people like the smaller size of the magic and wonder for getting around it. but it has the fewest extra facilities (one speciality restaurant versus two). I find the wish (and presumably the treasure) to be the most 'themed' in its lounges, if thats important to you. simply amazing. the dream and the fantasy are the goldilocks in the middle .. they have a lot of the newer features but fewer guests than the wish or treasure (but more than the magic and wonder) for when you go off ship to a private island.
8) I havent said a lot about the itineraries because those to me are an aside. the ship is the main attraction. I skip Nassau all together. thats not a bad thing, staying on ship on port days can be fun, less people. I liked grand cayman, Tortola, and st. johns.
9) this is going to be controversial... but if you can afford it, do consider concierge. There are a lot of people that will tell you its a good value, and they are right, from a dollars and cents point of view it wont add up, but for sheer comfort and feeling pampered, it is simply amazing. if your wife is a coupon cutting bargain hunter, she might not be able to look past the cost, if she likes to be spoiled, concierge is worth considering. the advantages are numerous but they really do help you with all your on board decisions and you often get access to splurges that are sold out. and if you want a cabana on their private island (and I do recommend it for the splurge), really unfortunately most if not all are scooped up by the concierge guests (they get first choice on everything)
10) I like to stop by Disney World with my cruise. Port Canaveral is the easiest, but its just a 3 hour drive from Fort Lauderdale which I don't mind doing, so I chose more by the itinerary. conventional wisdom is the park first and then relax on the cruise, but any day at the park is a good day to me, so I find the order doesnt matter. My favorite stay was to go from a cruise to a stay at the Polynesian, felt like just continuing the vibe. but I love the poly so...
thats all I have to say, no doubt will think of something else. the suggestion of a
travel agent is a good thing, but do not be shy, if you aren't clicking with the one you are assigned, ask for another. there are some great travel agents, and then, some who are less great.
