First off, the apprentice didn't survive the first game. He died. He died in the game, and he died in the novel. Palpatine killed him, causing him to die. After he died, he was dead as a direct result of being killed. The real question is how he is alive again.
I personally think that it should be a clone, because I think it's the most plausible in-universe explanation. I can't fathom a reason for Vader or Sidious bringing him back to life (even if they could), and they're the only people whom anyone would ever have any reason to believe could or would. However, I wouldn't put it past Sidious cloning him as some kind of experiment (since the clone wouldn't have any reason at first to disobey him) and having it go wrong somehow.
"Grant Allen [...] had written a book about the Evolution of the Idea of God. [...] it would be much more interesting if God wrote a book about the evolution of the idea of Grant Allen." ~ G. K. Chesterton, The Everlasting Man