I think the way to bring in Scott is to have a montage of Xavier using Cerebro to recruit new mutants. So we see him using Cerebro, and in Cerebro we see a quick shot of the mutants he's recruiting, and then afterwards have a shot of all the new students together, being greeted at the mansion by Xavier.
I think this works on a number of levels:
-It doesn't toss out continuity of X-Men Origins: Wolverine and how Xavier found Scott.
-We don't need to go into detail of something we've already seen a few times in the movies already, of Xavier meeting every student individually to recruit them for the school.
-We can introduce many different characters to the school - ideally characters like Storm or, even more specifically, Jean Grey. If Vaughn (or whoever ends up making the film) doesn't want to introduce more than one major character, then the new recruits can play a role very similar to than of Jean Grey in X-Men #1 - a new mutant, a new student, who isn't exactly a member of the X-Men yet, just a very promising student at Xavier's school (correct me if I'm wrong but I don't believe that Jean Grey is part of the battle against Magneto in X-Men #1). At the same time, we can, without going into huge detail about it, see the beginning stages of the relationship between Scott and Jean.
-Cyclops doesn't have to come in and instantly become the leader. But perhaps that can be part of the rivalry between Havok and Cyclops. Cyclops has natural leadership qualities, but Havok being older, and an original member of the team, feels that he has more of a claim to the leadership role.
-While Cyclops wouldn't be the *ORIGINAL* X-Man, he'd still have a sense of claim to the "1st student" role, as Scott could be the first student recruited by Xavier after he actually starts the school. While Banshee, Havok, and Beast will have the claim of being the original X-Men, Scott could still in a way be Xavier's "first student". If there was a 3rd movie, he could already be established as a student, and the 3rd film could see the eventual departure of Banshee and Havok perhaps, forcing Scott to step up in his leadership role, while bringing his new team of Jean Grey, Storm, and Beast with him. This would make a 3rd movie in the First Class series consist of Cyclops, Storm, Beast, and Jean Grey, which is a first class team I can get behind. The movie could deal with Beast becoming more involved in the political realm, leaving the school at the end of the movie to fight for mutant rights in a new way. The movie would end with Cyclops, Storm, and Jean Grey being the current X-Men team, which then segues very nicely into X-Men.