I found the majority of this season to be really well-done (though not without its issues). In particular, the future Big Three of Clark, Lois, and Lex were very neatly moved into their respective emotional positions quite handily and Lana and Clark's relationship had a more graceful finish than it had before.
I have issues with both Lana and Chloe getting forced into the 'helpless damsel' position in the finale, but both of them do get to be more than that often. It doesn't define them.
The Lex/Clark scene was really great. I like that Lois reminded Clark that he'd seen so much to like in Lex earlier in their lives and the dialogue in the Lex/Clark scene was the right mixture of self-righteous "I'm doing this for the planet" and wounded "why didn't you trust me?" from Lex and an appropriate response from Clark, who cares but who has come to realize that Lex was fully responsible for his own moral choices and does not get to hang those on Clark.
I'm not sure that cheering and rewinding to watch again was the response you wanted this member of the audience to have when Ruby called Dean a spineless dick and clocked him one (and then some more). I kinda hope that it was, but since you had Sam adopt Dean's favorite gender-based insult in this episode, I doubt it just a bit. Also, it may be a bad sign that I mostly felt a deep sense of satisfaction at seeing the hellhounds tear Dean up.
On the plus side, you've killed off both of your reoccurring female characters! Oh, wait, was that a plus or a minus? I always get those mixed up.
P.S. I quit Prison Break over this kind of bullshit. My viewership is not guaranteed.
P.P.S. Also, see Terminator: The Sarah Connor Chronicles for notes on how not killing Henriksen might have been a good idea.