We write a fan fiction like this! It's really intriguing and thought provoking. There are some ideas I really like, and others that I would alter just slightly.
The idea of an evil clone sent by NEMESIS is growing on me. However, I dislike the proposal that she is just NEMESIS in human form with all the collective memories and malice. I also don't want the clone to be a direct reincarnation of Elisabet or a vessel for her memories. I think all 3 deserve to be separate entities.
NEMESIS should stay as an AI bent on destroying life (giving NEMESIS life feels weird). If Elisabet's mind is alive within NEMESIS, I want it to stay digital. If NEMESIS created a clone, she would be a tool to be used for its personal agenda - a way to interface with ZD technology. I draw parallels to the way Aloy was a tool for GAIA and Beta a tool for the Zeniths. All 3 brought to this world to fulfill a certain goal that none signed up for.
I actually like your idea of a (somewhat) nihilistic clone. Clone #3 will be raised by NEMESIS and idolizes Elisabet Sobeck. NEMESIS would have manipulated her by saying that, "The Earth has been corrupted by war, religious extremism, and loss of history. The only way to save it is to destroy all of society and rebuild it anew." (Funny, that sounds like something Sylens would say.) Clone #3 believes this wholeheartedly because of a Stockholm Syndrome complex and because Elisabet was willing to condemn her world in the hopes that a better one might be built. In this way, she becomes more complex - not quite evil but definitely misguided, and enough for Aloy to pity her. She still has to fight "a darker version of herself" in the end though.
I'm also imagining a subplot about emotional blackmail. The clone can reveal to Aloy and Beta that, "If we agree to help NEMESIS, then NEMESIS promises to reincarnate Elisabet Sobeck for real, memories included. We can have our mother back. We can be a real family. And we can create the world Elisabet wanted, free of war or suffering." Naturally, NEMESIS is lying, but it's still fits the character in my head.
What do you think? I've been following your comments lately, and they are really fun to discuss and fantasize about.