1. Magneto not putting his shield up was PIS.
2. Storm's attack didn't do much to Magneto except fatigue him faster. He wasn't like, "I can't breathe! I'm suffocating!" he was like, "Man, I'm getting kinda winded. I wonder why?".
3. He'll end the fight before that becomes a factor, or
4. just put up his shield and be done with it.
5. Storm's trick only works in confined spaces where you can lower the air pressure in a room. We're not fighting in a confined space, so
6. Magneto could just fly away from the vortex.
No, sorry, too many options for Magneto to not be affected by that, and all he has to do is fling Storm into space by the iron in her blood. Or mind control her to stop. Or blast her to hell. Or snatch Polaris' power away. or mind control Bishop to blast her. Or whatever the hell else he wants. Storm isn't affecting this fight, I guarantee.
This fight is still a horrible, horrible mismatch.