I think there are a couple of reasons why.
For one I felt like I wasnt as attached to the character as I was in 3. I really had no idea as to who he was. What his life was like. I understand that they wanted to go through and have you really create your own character, give you a clean slate, but this doesnt always work. Yes, they give you information later on, but its basically "this was your job," and even then, I personally felt like it took almost to long. By the time I reached the explanation from Mr. House, I really didnt care as much for my character as I did the rest. I really like the way this video explained it:
http://www.escapistmagazine.com/videos/view/extra-credits/2681-Amnesia-and-Story-Structure
Second, I felt the map wasnt as well done. Yes, they are very similar. Yes, they are both waste lands. But 3 had some more in it. You had the dessert type areas, and the cities. And I felt like there were more places to visit. You walk 3 minutes and you have found someplace new.
Third, although I think the whole multiple factions was a great idea, I was disappointed at the end. All it pretty much did was decide who helped you at the end.
So these are basically imo. I thought it had some improvements, but it also had some areas where it just wasnt as good over all.