I would argue that Alien Resurrection is a mutation rather than a betrayal. That although Alien Resurrection doesn’t follow the same linear, canonical, path of the previous three, it is only guilty of going off at a tangent – and that only by of virtue of necessity.
This film is a mutation about mutation – and I wonder whether it isn’t in its narrative about mutation that the feelings of betrayal may emanate. The theme of mutation is born out of necessity: the death of Ripley on Fiorina ‘Fury’ 161. She is cloned from remains, but this has resulted in the contamination of Ripley’s DNA with the alien, she has become a hybrid. And it is this cross-cloning which certainly begins our unease, we have lost our human touchstone. The hero is no longer dependable – could this be what provokes the notions of betrayal? Unlike the saintly Ellen Ripley created through the previous trinity (an incarnation of human purity, even when defiled by the alien, in Alien3, she sacrifices herself) this incarnation is unrecognisable, we can no longer trust her, her motives are selfish, she is only part human, and is most definitely part alien.
But Ripley has only been mutated, surely that can’t equal a betrayal. Alien Resurrection is only guilty of changing the hero we had grown accustomed to, by the end of the film Ripley exepmlifies human characteristics; the compassion for the even more mutated previous clones, the maternal bond with Call (recurring theme from Aliens). And far from being a betrayal I think it is a worthy mutation – one which Magneto would argue, by virtue of being a mutant it is the next level of the evolution of the Alien canon.