Cassandra Nova is Charles Xavier without a filter—no compunction to not use her vast powers for anything other than her singular goal: revenge against her brother. She literally sustained herself after her stillbirth out of her hate for him, so… it’s a lot!
But Cassandra’s effectiveness as an X-Men villain is because she’s the rare character introduced as actually achieving her initial goals. Cassandra’s very first act in the comics is to manipulate a surviving cousin of Bolivar Trask, the architect of the Sentinel program, so she can swipe his genetic material for herself, activate a Sentinel Master Mold, and use it to produce an array of Wild Sentinels that she immediately unleashes on the unwitting mutant populace of Genosha. Within hours, 16 million mutants are dead at her hands—a genocide with such horrifying, long-reaching implications that even in the ever-fluctuating continuity of superhero comics, Marvel’s mutants are only barely just beginning to really recover and move on from it.
Even beyond her opening act being the near-extermination of the mutant race, the first few arcs of New X-Men involve Cassandra’s revenge plot spiraling wildly out of control on Earth and in space. Although seemingly killed after she’s brought into Xavier’s Mansion for interrogation after kickstarting the Genoshan Genocide, Cassandra psionically swaps her consciousness into Charles’ body while placing his into her genetically sabotaged physical form, hoping to kill him while she puppets his body about. She infects the X-Men with a nano-sentinel virus that nearly finishes the job of exterminating Charles’ top students, and even manages to flee to space with the Shi’ar and destabilize the Empire along the way—almost convincing Charles’ on-and-off-again lover Empress Lilandra that Earth’s mutants have been infected with some kind of insanity plague, necessitating their total destruction.
Cassandra’s immediate legacy even beyond this shaped so much of what was important in Morrison’s work on New X-Men: through her, they established the concept of the Secondary Mutation, they set the stage for the worldbuilding of mutant culture and their presence among human society, sparked by Cassandra/Charles’ revelation of their mutant identity, that Morrison explored throughout their time on the book. Cassandra’s revenge spree also in part establishes actually setting Xavier’s School as a campus where hundreds of students live and learn—a de facto that would persist throughout the 21st century. Despite not actually taking that much page presence in New X-Men’s early arcs, Cassandra is a character that fundamentally shapes so much of that comic’s run—and in doing so helped establish New X-Men as one of the defining and influential runs in the franchise for the new century.