It is Susan. If you go to the information about Desperate Housewives on imdb and to season 5 and it specifies very clearly that he marries Susan not Katherine, so it seems very conclusive that he eventually chose Susan. Hope that helps.
I think he marries Katherine. I have seen a pic of susan and Katherine in wedding gowns and the one Katherine wore was the same one as the final episode. Sorry I wanted it to be Susan
He married Susan
susan
yes
susan