Illness prevents me from entering any tournaments at the moment, but when I get better, I intend to return and plan on using MM as a counter character. In the interests of full disclosure, let me explain.
Megaman can counter Magneto with the glitch. His stand jab, stand short and low jab all come out in 1 frame. The worst that can happen is that you trade, so you don't have to worry about guesswork. If you hit Mags while he's on the ground, best combo is to go into stand forward xx uppercut, unless you're really confident in which case you can go ahead and do the air combo.
The trick is finding a good Megaman team. Megaman/Storm/Sent would probably be the best, but I admit that I use AAAs as a crutch. Megaman/Cable/Commando or Megaman/Storm/Commando would probably be what I'd go with.
The goal would be not necessarily to win the whole match, but to get 1-0 on the opponent. If they're smart, they'll probably counter you with some Cable configuration, in which case you are free to tag to MSP or some other rushdown-centric team. The whole point here is to get that 1-0 advantage.
And, yeah, maybe I'm dumb for revealing a trump card like this, but I'd feel easier not hiding shit. So, roll some ideas around.