If I recall correctly, AoA Magneto was only half as powerful as 616 Magneto, since AoA Magneto used so much of his power to take out Apocalypse's Celestial starship prior to the events in seen in the 90s AoA books. He never regained that lost strength, and it's one of the reasons why Magneto and Apocalypse's final battle was so prolonged. In 616, Magneto (by all measures) should trounce Apocalypse.