Gemini 3 Shepard and Stafford as it was supposed to be, Shepard was removed before the rest of the flight schedule was finalized.
The question for Apollo is two fold, i) when does Shepard transition to Apollo. Historically, the early Apollo CDR (Grissom before he died, Schirra, Borman, McDivitt) all went to Apollo pretty soon after their Gemini flight, while the middle CDR (Stafford, Armstrong, Conrad) returned for second flights as or served as backups for later Gemini flights. The ii) does the Apollo 1 fire still happen, and the program gets delayed by 20 months as it did OTL. This delay permitted the remaining people in Gemini to finish up their missions and train on Apollo, people like Stafford, Armstrong, Conrad, Young, Lovell etc. As well as the Group 3 Astronauts who flew as Pilots on later Gemini flights (Scott, Cernan, Collins, Gordon, Aldrin) to complete training on Apollo (these guys along with Young and Lovell would provide most of the CMP and in case of Cernan, LMP for early Apollo flights).
If both of these things happen as in OTL, then the chances are few changes, probably Shepard instead of Borman gets the first Lunar sortie. If either of the two changes, then its unrecognizable.