-It doesn't have the strong ending of the original. Bit of an anti-climax, too, where in the choices you made don't really feel like they matter. The game boasts that it has multiple endings, but they're extremely minor variations, which contrasts badly with the divergent storyline.
-It's a lot shorter then the first game, with just three acts.
-They set up a lot of plot threads that don't get resolved and are instead left open for the third game. Normally I don't mind that, but the way it's done here makes it feel like half the story is missing. Some characters even just disappear without too much of a send off! And the stuff they set up is far more intriguing then the Assassins of Kings plot (which at least has me excited for Witcher 3 because it really is BIG).
Not to say that it's a bad story; it's not, and it does some things that other RPGs definitely should take notes from. And when it's good, it's fantastic. But those issues really brought it down for me, and when compared to the first Witcher, it's just not as strong.