Breaking Bad season finale was a treat. There are very few shows that can really do what this show does. Every episode is tense and the writing is truly amazing. I don't know if the writers had all of this planned from day 1, but it sure seems that way. Everything flows together, from season to season, and just like in real life, there are no black and white characters. Everyone is a varying shade of grey.
Found this interview with the writer, Vince Gilligan...interesting to read about some of the very things I had just written above. Warning - Spoilers included in the link.
Here is the link to the official site at AMC where you can get more information.