The hints are rather clear. Jack is a time traveling person who is still effected by ageing, thus being incredibly different after x period of years, possibly millions. The show seems to signify the way he looks is due to him ageing past when he should have. Jack would not have commented on his gray hairs if they didn't tie in to the fact that he is still being affected by time, even though he can't die. In the Torchwood series Jack is killed countless times by a personification of death itself, which may be why he ended up being capable of dying.
So, listing the facts, Jack is a time traveler, Jack ages like a normal person, Jack is possibly immortal, Jack died countless times to a death creature. It all seems to line up for why after millions of years or more he looks very different and can die.
He even asked what would happen to him if he kept ageing while being unable to die, lol