Some of the fanboy contingent are complaining about how parts of Season 2 deviate from the narrative in the books, particularly the Arya and Daenys plotlines. Personally, I think that most of these changes are for the better, since one of Martin's literary flaws is narrative incongruity and illogical character motivations and actions. As long as he keeps the main plot points moving forward, the little changes are fine with me.
Season 2 will probably just finish book 2. Now, if the producers don't pander to commercial concerns and instead leave the important set pieces from Book 3 as they are, Season 3 could be the best one of all. Everything that happens in the books after it pales by comparison.