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.
"There is something going on in time and space, and beyond time and space, which, whether we like it or not, spells duty." -Winston Churchill
"For of all sad words of tongue or pen, The saddest are these: 'It might have been!'" -John Whittier
"Apathy is death." -Kreia