At best one can draw only slight parallels to the plight of the Jewish people in the lead up to and during World War II. The base premise of the sequel is this: Jeff Bridges in a dual role is both Kevin Flynn "The Creator" of "The Grid", a digital world populated by computer programs of various types, and Clu (Codified Likeness Utility) a golem-like version of his younger self. Clu, in essence, is the caretaker of the vast virtual world whose primary function is to "perfect" the system.
Exceeding his programming with a glint of free will and left unchecked by Flynn, Clu lusts for total control to achieve absolute perfection. Enraged by "The Creator's" embrace of the ISOs, (Isomorphic Algorithms) non-native yet still code based entities of the digital space who are seemingly imbued with the potential to "change the human condition", Clu lashes out.
Sounds more like what happened between Ramses II and Moses in the Passover story when Ramses the first preferred the son of the Hebrews slightly over his own flesh and blood.
I will say this of Leibovitz's comparison of Legacy to the Holocaust. Clu committing genocide in the great purge against the ISOs, blaming them for various glitches damaging the established society, then marshaling an army of devout followers to even further reshape the real world, is the strongest parallel to Hitler and his rise to power. Hitler scapegoats the Jewish people, for ills that befell the German economy. Hitler's action taken to try and correct it was a similar 'purge'...the final solution, death to the Jews.
Legacy is more the story of a son wishing to put what is left of his family back together by rescuing his father from his 20-year, self imposed imprisonment within the computer-generated world. Even the 1982 original film's creator Steven Lisberger focussed only on the battle between good and evil and not projecting into the film the conflict from his past that his father, a German Jew, had been placed in a concentration camp by his mother's family.
The baton of knowledge on the potential of the grid, passed from father to son, and the actualization of one's true potential are what I believe to be the core messages of the film. What say you?