the script changed considerably when Mangold was named director. The original script written by McQuarrie had one mutant in it...Wolverine, and was extremely close to the original arc by Claremont and Miller. As has been mentioned before in here, Mangold said that script is about 80 percent intact, and of course we know from the trailers now what changes have been made. It's still fairly close, but slightly altered.
Also really this is the second movie that is part of the new initiative. The first of course was 2011's "X-Men: First Class".