I just read "Wars End" by Chuck Sweeney, the pilot who dropped the fat man on Nagasaki and he briefly mentions that the B-29 was the only plane capable of dropping the bomb over Japan. Due to the secret nature of the B-29, did scientists at Los Alamos have a plan for deploying nuclear weapons? Were they made aware of the B-29 before it became public, or did they have other plans to actually drop the bomb?
The B-29 was not all that secret relative to other aircraft of the time, and was not designed with the purpose of carrying nuclear weapons in mind. The B-29 was simply the logical next step of the US's heavy bomber program that had been in place since the early 1930's. It was a continuation of the famous B-17 and B-24 designs, and was larger with more powerful engines to carry a heavier load of (conventional) bombs further, as well as a pressurization system to enable flight and bombing at higher, safer altitudes. It was a conventional bomber, meant to conduct strategic bombing from high altitude in large formations using regular bombs.
This high altitude bombing was quickly abandoned after early raids over Japan because of the difficulty in hitting targets from that high up using unguided bombs because of the wind. Instead, the B-29's were shifted to low-level incendiary raids. Anyways, the point is that the B-29 was the USAAF's principal heavy bomber in the Pacific, using conventional bombs, and had been for over a year before the Trinity test in July 1945, and there was nothing new or secret about it then. For the nuclear program, ~50 B-29's were modified as part of an operation codenamed "Silverplate". These modifications mostly dealt with the shape of the bomb bay to allow it to hold the different types of nuclear weapons, as well as the removal of some gun turrets to save weight. It was these Silverplate aircraft, like the Enola Gay and Bock's Car, that were used for testing, training, and actually dropping the nuclear weapons. This was what was top-secret, because of the secrecy around the Manhattan Project.
The B-29 was the only plane capable simply because dropping the nuclear weapons needed a large, long-range aircraft with a heavy payload and a spacious bomb bay. B-17's and B-24's were ruled out because of their limitations in these areas, whereas other aircraft that could possibly have done it, like the British Avro Lancaster, were ruled out because of a desire to use American equipment in such a secret project, among other things.