I'm sure age had a roe in it. Heading into WM21, Cena was 27, while was Batista was 36. Cena had longevity in the business on his side. If Batista was a decade younger at the time, the entire wrestling business might be different today.
Vince wanted Cena and Orton to be the top guys from the start. Batista got the push against HHH over Orton because the fans wanted it so Vince had to go with him instead. Back then Vince listened to his audience.
Ignore all the Anti Cena stuff and think/look back at WWE at that time. Cena wasn't actually a chosen one, but he got so over and was making the WWE so much money that Vince had no choice to get behind him. They butchered the Cena character that got over mind you, but still.