^ It comes down to this...
For both Magneto and Apocalypse the X-Men have been the difference in thwarting their plans. Let's analyze what each has done, that was prevented by the X-Men:
Mags:
- He first attacked the US military base Cape Citadel.
- Creates Asteroid M.
- Conquers the South American nation of San Marco in order to create a homeland for mutants.
- Along with his Brotherhood he captured the X-Men.
- Creates the Savage Land Mutates.
- He opposed Doctor Doom's attempt at taking over the world.
- Involved in the Secret Wars (aligned with Xavier and the X-Men)
- Helps the X-Men defeat the Beyonder.
There are plenty of other schemes that he has attempted, but mainly Magneto has strayed between world domination (believing that there is no peaceful coexistence) and creating a safehaven for mutants.
Although he has shown willingness to kill those who try to stop him, he is acting because he believes he (and his kind) are under attack. He wants to rule, because (possibly correctly) he believes that home superior, are superior, or he wants to isolate himself and provide a safe existence for his kind. He believes that "a war is coming" and in order to protect mutantkind he must defeat humankind.
Yes, he has done evil things, but he has not done the kind of evil things that Apocalypse has.
Apocalypse:
- He transformed Nathaniel Essex into Mr Sinister and tried to get him to infect the world with a plague that would transmute them. He was defeated by the time travleing Cyclops and Jean Grey only because he was weakened by the betrayal of Mr Sinister. This forced him into his slumber, from which he wouldn't awake for almost 40 years. He likely would have taken over the world if not for Sinister's actions.
- He creates his Horseman with Angel as the leader Death, with the plans of destroying New York. Again, he was only defeated because Angel regained his senses after believing that Iceman had perished, and because the X-Men had help.
- He infected Cable with the technoorganic virus, sending Cable to the future where Apocalypse had taken over and ruled the earth until the 39th century.
And there are plenty more things that he has done. But the main point is that most of the times he has gone up against the X-Men (or other X teams) he was in a weakened state, or was betrayed to enable his defeat. In almost all cases it took multiple teams to defeat him.
The truth is, Magneto is just a man, while Apocalypse is something more. He is eternal and has powers way beyond what Magneto has. He's all about Survival of the Fittest. Yes, Apocalypse was effectively X-Factor's Magneto. And again, although Apocalypse believes that he is doing the right thing, the difference between him and Magneto is the desired end product and how to get there.
Magneto wants to rule or be isoltaed, in order to protect mutantkind, while Apocalypse doesn't care who dies in order to promote his ideal of survival of the fittest.
Also, here is something to think about...
Magneto was never able to take over the world, while Apocalypse rules in the future (until the 39th century) and also rules in the Age of Apocalypse universe, which deviated from the 616 universe because of Xavier's death. In other words, Apocalypse has and will win, while Mags never has or will.
Yes, in pretty much every list Magneto is considered number 1 as far as X-Men villains, but that's more because of his popularity and frequency. But in each of these same lists, guess who's number 2...
Here is a statement from one of those lists:
"Apocalypse represents perhaps the greatest threat the X-Men have faced"