So I know I'm super LTTP to the party on this but I wanted to chime in on how well this season was written. If there was one theme this season had it was
CONSEQUENCE
From the opening when Tuco beat a man to death for "dissing" him, all the way up the plane crash there were unexpected, and expected consequences everywhere. Jesse losing his house, well he said he'd never cook there. Consequence. Walter lying to his wife: consequence. Jane relapsing in to heroin and...ya know. Consequence. Her father's reaction and the plane crash: consequence.
Admittedly the final one was large even for TV but I think it says a lot for Walter's slip in to evil. He will not admit the consequences, both close and far reaching, for his "stepping up" of the drug trade. Like many teacher's and scientists he's about the numbers and the end results. The season finale was a big fat not subtle in the slightest slap that he is going too far. Great show and really well written from a thematic view.
Fun Fact: I am posting here because I am just starting season 3 and don't want spoilers.