Despite delays due to technical problems and weather this plan was followed on the first three orbital flights: Mercury MA-6 (Glenn/SC13), MA-7 (Carpenter/SC16) and MA-8 (Schirra/SC19). However by Schirra's flight he seven-astronaut corps was down to four - Glenn, Carpenter and Slayton were off the flight roster (Glenn on President Kennedy's orders because he was a national icon; Carpenter because he had screwed up; and Slayton on medical grounds). So even thought the flight-ready SC19 had been delivered to Cape Canaveral on March 20, 1962, the decision was taken to cancel the remaining short-duration mission and move directly to an 18-orbit mission. Cooper was the only astronaut not yet to fly and would have been the pilot for the original MA-9.
Walter Williams, Alan Shepard, and others at MSC pushed for a three to six day Mercury 10 endurance mission. This would give America the manned space endurance record for the first time and also cover the biological objectives of the first two Gemini missions. The Mercury 15B capsule had already been modified for long-duration flight and Shepard had the name 'Freedom 7 II' painted on the side. But the risk and work pending on Gemini persuaded NASA managers not to undertake another mission unless Mercury 9 failed. The massive breakdown of nearly all systems aboard Mercury 9 convinced NASA that this was the right decision. Their risk assessment was also influenced by Martin Caidin's novel, Marooned. In the book, Mercury 10's retrorockets fail, stranding astronaut Pruett in orbit. He is saved by the combined efforts of NASA Gemini and Russian modified Vostok spacecraft. Such resources were not available in real life. On June 12 NASA administrator James Webb told Congress that there would be no Mercury 10 mission. It would have only cost $ 9 million to fly the mission, but deleting it freed up 700 workers to concentrate on project Gemini, which was behind schedule and over budget. On June 13 McDonnell's remaining contract work for Mercury was terminated.
In actuality astronaut Shephard was removed from flight status in October 1963 due to Meniere's syndrome. So if Mercury 10 had occurred, it might well have been flown by Cooper.
If SC12B had flown on a long-duration flight it would have been crewed by Grissom. Given the plans to follow SC15B for three days, it probably also would have undertaken a three to six day flight. Grissom was however already deeply involved with the follow-on project Gemini. It is likely that, as a test pilot, he considered commanding the first manned Gemini flight a far superior assignment to spending several days in the cramped, trouble-prone Mercury design that had already tried to kill him once. Cooper would have been the only available alternate pilot.
When Schirra's Apollo 2 / AS-205 mission was cancelled in November 1966, the booster went to McDivitt's mission, and it was called AS (or Apollo) 205/208, or AS-258 (before Schirra's cancellation, McDivitt's was AS-278, because it used Saturn IB boosters 207 and 208).
The mission was finally flown in July 2005 with Andrew Thomas, Lawrence, and Camarda flying instead of Malenchenko and Lu. No crew change was accomplished; instead the primary objective was to verify fixes to the shuttle external tank and test heat shield examination and repair techniques. Station resupply was accomplished, but was secondary.