We all know Magneto is a badass villain and a powerful adversary at Marvel: Avenger's Alliance PVP. All of his relevant stats are between above-average and excellent. With some Iso-8 Crystal investment you can transform Magneto into a PVP sweeper, given the right team combination.
This discussion will be rather simple since Magneto in its own right is a powerful adversary. We will just focus on optimization for him to work optimally at PVP.
Let's first make a brief review of Magneto's awesome passive abilities.
Mental Shield negates any kind of psychic attack. Period. This means Emma Frost won't be doing much against him, besides War Diamond.
Flying is always welcome to evade massive ground attacks from Captain Britain and such.
Master of Magnetism is the real star here. This passive does a number of different things. The most notable and useful is that it automatically applies Magnetized to any metallic target. This means robots, armors, Wolverine and most Agents will be Magnetized. This passive ability is so good that even if Magnetized is removed from a metallic target, Magneto will automatically refresh it. Magnetized is incredibly useful because it won't allow targets to evade or critically hit. This is immensely important in PVP, where the metagame has shifted from damage-over-time-effects to critical-hit-sweeps. Master of Magnetism also enables Magneto to randomly preemptively counterattack any Magnetized target for massive critical damage. Master of Magnetism also prevents Magneto from being Magnetized by opposing Rescues or Magnetos and gives him the ability to critically hit any magnetized target. Note that Rescue won't negate Magneto's critical hits since he is immune to Magnetized.
It is easy to assume that Magneto's most important ability is to Magnetize targets and critical-hit them for as long as they remain so. To make him even more interesting, his moveset takes advantage of his ability to add even more adverse effects, like Stun, and deal even more damage.
We will start with Magnetic Shield, since it is just a supportive move, more than a part of the core strategy for Magneto. Magnetic Shield is similar to the gadget Magnetic Field Generator. It envelopes your party in a protective Magnetic Shield that grants Magnetic Acceleration upon removal, which means your Agent or hero will be able to take an additional action that turn. Pretty sweet ability that's very situational. A momentum builder and life-saver most of the times.
Magneto's other three moves are attacks that are guaranteed to critically hit when the target is Magnetized. Magneto is so generous that one of his useful passives, Master of Magnetism, already inflicts Magnetized on any metallic target. Magneto's first attack, Electromagnetic Blast, also Magnetizes the target. This, however, can be a little time consuming for non-metallic targets. With the popularity of Rescue's Status Reset ability and Scroll of Angolob, Magnetized won't stick for long on non-metal targets. This can severely hinder Magneto's ability to sweep at PVP.
The answer to this problem is fighting fire with fire. Magneto's best teammate would be Rescue because she will Magnetize ANY target, be it metallic or not, for as long as she is defending with her Magnetic Attraction ability.
With Rescue by Magneto's side, the enemy team will almost always be Magnetized. Magneto will be able to critically hit with his attacks. When the whole enemy team is Magnetized, you just need to repeatedly volley with Graviton Well, a powerful area attack that will critically hit any Magnetized target. With this Magneto will be able to quickly decimate opposition.
If you are presented with a more complicated situation, like facing an opposing Magneto or a Defender, you may want to use instead Electromagnetic Blast. This single-target attack does three things: 1) Magnetize the target, even if it is non-metallic, 2) critically hit any magnetized target and 3) randomly deal preemptive damage against Magnetized targets with Reverse Polarity. This is the best way to micro-manage pesky opposing heroes that won't let Graviton Well work properly.
Agent (Scrapper Trench Coat)
Magneto (Tactician) Rescue (Tactician)
The only real problem with this team is that you have two Tacticians in it. Any experienced PVP competitor knows that having repeated classes in your team is usually a bad idea. Thats why you need to use a Scrapper uniform on your Agent to counter the advantage that any Infiltrator may have against your two Tacticians. Also, since Rescue's Flyby attack can negate counterattacks on the target and Magnetized won't allow enemy critical hits, you may not need to worry to much about Infiltrators raping your strategy. For Bruisers gaining enraged on your Scrapper, just focus your assault on it first. If there is more than one, Protect with Rescue, remove the Enraged stacks with Status Reset and, if things go awry, just let them kill your agent so that they gain any more class bonuses.
There you have it.