Bishop says Magneto never leads the "X-Men" in any future he's seen. There was an alternative 1990s caused by Xavier being killed in the 1960s before he could prevent tensions between humans and mutants from escalating into all out war. Magneto lead the mutants in this war, but they were NOT the X-Men.
It makes sense that Storm is left behind to help Magneto; she can super charge his magnetism powers with electricity, if necessary.