It's a fact that in stories the villain you thought was well and truly dead might just come back for a sequel. There have been many different justifications proposed for doing this, from you only thought they were dead, to actual supernatural resurrection, to ultra-tech body reconstruction. If you're going to do it, try to come up with something original.
Or maybe just... don't explain it in any way whatsoever! If it's a game, you can actually leave it as a mystery for the players to try to solve.
Commentary by memnarch (who has not seen the movie)
You know, I just realized something. This whole cloning process being used works really poorly compared to the Kamino clones. The Snokes looked just as damaged as the first one we saw. Palpaclone has the baggy face skin from the Original Trilogy, and now also has probably blind eyes and something probably wrong with his hands. I guess it wouldn't be too far-fetched to say that the Force Lightning damaged his genetics and this is just how he looks now, but that doesn't seem Star Warsy, even for the Sequels. And a duplicator machine is right out.
I'm sure this scene makes very little sense in the movie. Like, we've had the clones shown off, the giant fleet coming up from the ocean, and Kylo is threatening Palpaclone again for some reason. If getting tossed down a huge pit into a reactor, then the reactor exploding along with everything nearby didn't kill him, what's a lightsaber going to do? There's probably a half dozen other clones ready for him to jump into as well.
For the Comic plot, I wonder if the Japor snippet is also acting like a tether for Anakin. He might have been weakened by Luke Force Transcending with the lightsaber, but the snippet still gives him the ability to interact with the world as long as it exists. And Kylo getting even partially possessed could also be a fun thing, assuming the movie is crazy enough to allow scenes that fit that idea to happen.
Transcript
Kylo Ren: Impressive. But I’m not here for a guided tour.
Palpatine: Tragic. I even had a gift bag prepared.
Kylo Ren: There’s only one way you could have survived the second Peace Moon.
Kylo Ren: The Japor snippet.
Anakin’s Voice: How do you know about that?!
Kylo Ren: ... Snoke told me.
Palpatine: Yes... the snippet. I put it in Vader’s helmet to keep her alive.
Palpatine: But after she threw me down the reactor shaft, my need was the greater.
Palpatine: I struggled out of the pit and hid in the shuttle while Luke was distracted by Vader’s death.
Palpatine: And took the snippet to sustain my recovery.
Kylo Ren: And now you’ll give it to me.
Anakin’s Voice: Yes... Yesss... Give it to him.
Palpatine: Wait, what?
Anakin’s Voice: Give it to him.
Palpatine: Very well.
Palpatine: But I must warn you. The warranty expired half a century ago.
Kylo Ren: {looking at Palpatine’s shrivelled face and bony, broken fingers} You know, that explains a lot.