Because they would have had to either make the system bigger, or make the battery smaller, neither of which would be a good thing. (Don't believe me? Look at a 3DS teardown, there's really no room at all in there for a second Circle Pad. Nintendo packed the 3DS to the brim.)
I think the new Circle Pad attachment is a good thing. It gives you optional (key word) dual analog controls if you want it. If you don't, you don't need to use it. It's a completely optional device. And it's not as big and bulky as it seems. People are saying that it's pretty compact and very light, and it feels really good in your hands (this is especially good for people with big hands who say the 3DS gives them hand cramps).