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This happened with Sonic Boom, also.
Bob Rafei was the concept artist for Jak and Daxter and left Naughty Dog when Uncharted was starting. He went on to found Big Red Button, the game company that created Sonic Boom. He was the director despite zero game design experience.
You can really see his influence on the characters designs, though- the scarves, the random bandages, the goggles- he just repeated his successful ideas from Jak and put them in a Sonic game.