We've done it both ways. We enjoyed the freedom of being independent of any pre-arranged booking, other than the flights, and we tried the ordeal of being treated like a parcel by an organized tour...
In spite of the convenience and arguably peace of mind offered by having all the details scheduled and confirmed, the true sense of freedom is replaced by a constricting feeling of regimentation. Time becomes money to be made by the tour operator and the staff, driver, guide, cook, porter, guard, dive master, etc. They all seem on the clock while I am trying desperately to feel liberated and out of time...