Apocalypse was meant both in the comics and the series to be the X-Men's deadliest foe: the ultimate Mutant.
But it's really a surprise how he's defeated easily in both.
And Magneto is more powerful than people think. Guy's powers aren't even limited to metal. He can move things like wood.
I'm not sure if he was "meant" to be their deadliest for (he appeared primarily in the spin-off X-Factor book for 6 years before making an appearance in one of the official X-Men titles during X-Cutioner's Song). He certainly has evolved into one of their biggest threats, or should be. My personal list of what the "Big Five" for X-Men "villains" should be are (in no order): Magneto, Apocalypse, Mr. Sinister, Mystique, and the Sentinels.