Some Magneto clone beat her again more recently in a Grant Morrison issue that most people say is one of the best arcs in the last 10 years. Wanna call that crap writing too?
So now you're saying that Ryu could beat Magneto???
No comic is completely logical in many issues. Creative teams change, and each creative team has their own view of the characters and they write according to that view. Sometimes their views contradict each other. That's the nature of an ongoing series of any kind - from Soap Operas to anime to the Fantastic Four to X-men. Dr. Doom stole Galactus' power, yet he lost to Squirrel Girl. I don't see your point in mentioning continuum.
As for the Magneto vs. Phoenix fight - it's not a matter of who is more powerful. Magneto didn't win because he's more powerful. He won because he's smarter and more resourceful. He drew upon all the EM energy of the entire planet and took it to her, causing her to shut down and suck the life right out of her. That's pure skill. You have to look past trading card power levels and look at the character himself - Magneto is as deadly as he is because he's good at using what he has, not because he can overwhelm you with his might.
Magneto beat Phoenix...twice. Phoenix is more powerful than Bison. Ergo, Magneto beats Bison. Not that hard.