One thing that I think will be a challenge will be, given how I expect things will unfold at Winterfell, how will they deal with the relationship in the third season between Roose and Robb, or more particularly, if we the audience are privy to the events at Winterfell, how will the writers maintain the element of surprise about a certain celebratory event at the end of book three, and who participates in it.
I think the book (spoiler)
blamed the sacking of Winterfell on Theon, but I could be wrong? Ramsay had supposedly captured him & brought him to the Dreadfort to await Robb's justice. My memory may be hazy, though.