I am well aware of Magneto's feats. I know everything you've posted here and stuff you didn't post. Dollars to donuts I know Magneto a whole lot better than you do.
1) Storm and Magneto have fought solo serveral times. Magneto even admitted that Storm has the power to beat him if she didn't hold back.
2) Magneto has NEVER wrested control over lightning from Storm. What Magneto was able to do was create a magnetic field above Storm's head which attracted bolts from the sky taking Storm by surprise with this. (This was TOTAL PIS, by the way). According to the story, since Storm was caught by surprise when she was hit by the bolts, she was harmed by the lightning. It was while she was severely injured when she tried to wrest control of the lightning from Magneto. At this point, her control over the lightning was greatly diminished because of her injured state of body. Storm's powers are limited by the force of her will and body as well as her unity with life itself. As a matter of fact, in her fight against Proteus, she was so badly injured that she could not even summon lightning and had to rely solely on wind. So, this just goes to show in the Storm/Magneto instance that Magneto was only able to resist Storm's attempts to take away the lightning from his control ONLY because she was badly injured beforehand. Magneto didn't even had enough control over lightning to be able to call them down directly. He had to warp the EM fields to create a charge to attract the bolts from the sky. Storm's power and control over lightning far oustrips his as she can take direct control of the bolt to call them down intead of the indirect way Magneto did it.
Now is where the PIS comes in. In Uncanny 117, it was established that Storm can detect all natural phenomena BEFORE they come into being. In other words, Storm should have been able to feel those lightning bolts before they came into being meaning she should not have been caught unawares by them. Secondly, in Uncanny 121, Storm was able to track Vendicator via the very faint energy signature he left in the atmosphere sometime later after he had traversed through the area. In other words, Storm should have been able to feel that huge magnetic charge Magneto put above her head to attract those bolts from the sky in Uncanny 150 meaning the whole way she was caught by surprise by the bolts in Uncanny 150 which harmed her was PIS from start to finish. To recap, first, she should have been able to sense Magneto putting the field above her head. Secondly, she should have been able to feel the bolts before they came into being meaning there is no way possible for Storm to have been caught by surprise by any of this without these powers given to her in Uncanny 117 and 121 being completely ignored to prop up Magneto.
Regarding Magneto's power over related forces in the EM spectrum, his feats with them are so minimal that they aren't worht mentioning in a fight with Storm. The only thing I have seen him do with microwaves is project them from his hands to burn down a metal door. Big deal. That's not gonna do squat against Storm in battle. You mention the invisible light feat where he made himself invisible. Big deal! Storm could flip her sight to see the world as energy which should enable her to see the light being bent. Not only that, she could still find him via body heat, his energy signature, his movement through the air, his body shape, etc. She doesn't need to be able to see him visably in order to locate him.
Magneto has NEVER repelled a nuclear explosion with his own power. The only time he repelled a nuclear explosion was during "Magneto War" when he was plugged into that machine which boosted his powers. In the story you are referencing, Magneto fired off that nuke, he was not assaulted by the nuke, In other words, common sense would dictate he was a safe distance from the explosion itself.
On the other hand, a nuke is a joke compared to the power of Sienna Blaze, which Storm redirected.
Here's the thing, if Magneto is going to fight Storm, he would be smart to stick to magnetism. That's where his big feats are. That's where his powers are the greatest by far. If he were trying to use those other energies against Ororo, it would be very foolish as he's FAR too weak with those forces to pose any kind of a credible assault against Storm. Eventhen, his magnetic powers are too far below Storm's power class to be a threat to her.
For Magneto to be a credible threat to a team, Storm can't be on it and neither can any Phoenix Force wielder.