I don't think they are treating the other movies as gospel, as far as canon goes. I mean, emma frost was a little kid in wolverine, and that takes place way after this movie.
As far as the whole alex summers thing goes, there wasn't an actual need for them to mention he has a brother. Since cyclops isn't even in this, it has no real relevance.
In the comics Shadow King is the first evil mutant xavier encounters, and what inspired him to create the x-men.
http://en.wikipedia.org/wiki/Shadow_King