Black Panther is also decent against Magneto, though you'll have to learn the former's combos to play him effectively. Psylocke can also counter Magneto as she has multiple dashes and hits quite hard.

Beast, Magneto, Magneto, Wolverine, Apocalypse, Magneto, Xavier, Gambit Level 10 Xavier, Psylocke, Apocalypse, Psylocke, Magneto, Gambit, Xavier, Magneto Level 11 ...