Given how many of us imagine that Phelps will be chosen, it's almost hard to imagine the organizing committee NOT deciding that. Phelps + Retton could be entertaining because of the height difference, but there's not a person alive who could pair with Phelps without it feeling lopsided, I feel.
That said, the person who lights the torch is not necessarily chosen because they were such dominant athletes. In 1984, Gina Hemphill carried the torch in the stadium. I don't remember that she was a top athlete herself — I just remember she was Jesse Owens' granddaughter. The cauldron was lit by Rafer Johnson. Johnson only won a single decathlon gold medal but he was chosen for a big mix of other (good) reasons.