I would kind of like to see him with Xavier at the start of the movie. With his personality I could see him being a difficult person to lead, which would help with the Cyclops development.
About the mid point or so through the movie I could see Magneto, who has come to the conclusion (just like in the comics) that the best course of action is to isolate from the homosapiens. He is going to, and ends up creating Asteroid M/Avalon, a safe have for mutants (what an amazing scene that could be). He offers to take any mutants who wish to go, and he visits the X-Men with this offer. He also drops how he is Quicksilver's dad. This prompts Quicksilver to leave the X-Men ad join up with Magneto.
This does multiple things...
1. It would give us a cool Danger Room scene with Quicksilver where they can slow down time and what have you.
2. It allows leadership development for Cyclops, having to deal with the difficult, if not bored, Quicksilver.
3. It allows a reason for Magneto to visit and resolve certain things with Charles. It could even get to the point of "Charles, you were right. Violence was not the right way, but you were wrong, these humans will never allow us to live in peace as long as we remain under their domain."
4. It gives a reason for Erik to tell Quicksilver about him being his father.
5. It takes an overly powerful mutant out of the picture for the time being, allowing the focus to be on the X-kiddos.