There were several things they should have done differently, IMO:
1. NOT do the Jean/Logan "true love" thing. Their relationship has always been lust, and nothing more. "True love" just doesn't fit them. If they wanted a love story, they should have kept Scott.
2. Have Storm be the one in command. She should have had her be the commander in the final battle, and also changed around the "X-Men Board the Jet" scene. It was okay to have Logan challenge the kids initially, because he does have a skeptical nature. They should have had the kids step up to his challenge, though, and had Storm give the "pep talk."
Maybe some more later. Gotta run now.