Plot hole: Near the end of the episode, the part-human Doctor is said to have all of the memories of the original Doctor. If this is true, then the part-human Doctor should remember the time the original Doctor spent with Rose, so shouldn't commit genocide or need Rose to help him to not be a man of killing.
Plot hole: Davros said that the reality bomb would destroy all parallel universes. He fails in the Doctor's universe, but the Doctor said in an earlier episode that every decision creates a new parallel universe, like if Donna had walked out of the TARDIS with Jack, Rose, and the Doctor. She wouldn't have imbued herself with Time Lordness, so Davros would have succeeded. This means that all the universes, including the Doctor's one, should have been destroyed, because if the Reality bomb only succeeds in one universe, it would destroy all the others as well.