I love the storyline of William, it's kind of the only troubles we see Scully getting into this season.
My only complaint, wel not really a complaint, is that they make it seem so simple to give up a baby for adoption. I know that I wouldn't be able to give up a child of mine (if I ever have children) I think it's hell for a mother, espescially when you already had him/her with you for almost a year. But The story that they tell is great.
It also show the realationschip between Scully and Mulder at some point, she knows him really well, that's why she knows it's not him. If you want to know a person that well, you have to have a great bound with him/her (friends or otherwise) It's also very obvious that she loves him.