I would say that the two biggest factors are freedom and price. The do it yourself excursions are almost always less expensive then the Disney excursions. Also when you book yourself you often find yourself with smaller less crowded conditions (definitely true in our case). When we did the glass bottom boat in Nassau we booked through Disney. We had to meet early, wait in the bar for everyone, listen while the excursion was explained to everyone, all get on the same bus - had a set time to stay - all had to ride back at the same time on the same bus. If you do your own thing you have much more freedom. Captain Marvins you even walk to so there is no transportation to deal with. As for Chankanaab we took at taxi which was $10.00 each way and we had no problems getting there or back. I wouldn't hesitate to do it again. I even went without my husband and was brave enough to go for it! He stayed home with our 6 year old who is afraid of stingrays and dolphins. They just went to the local zoo and he was thrilled. Saved us money! At least until he is older...