I would clean the shoes with something like the Saphir Renovateur and then maybe try either a #8 wax polish or the cordovan cream that Kirby's Hanger Project or Epaulet sells. The Cordovan Cream will have more pigment in it so that would be my first recommendation. I think you should be able to even out the color of those shoes pretty well. I also wouldn't worry about the creasing unless it bothers you. I have several pair of shell shoes that crease differently for each foot. Now when I get new shell shoes I wear them around the house to determine where he creases are going to be and then I manually crease them so that the creases will be as uniform as possible.
Are you referring to the "pen method" here, or something different? I've never had much luck using the pen method, but it must work for many people, otherwise it wouldn't be recommended so much I suppose.