I finished the season last night (I only intended to watch two episodes, but that quickly made an out of control spiral into watching all four I had left).
It turns out I was a bit mistaken on the central theme. I thought it would be 'Dexter makes new best friend who is like him, and is forced to choose between new homicidal best friend and old well-adjusted best friend." That would have followed the same forumla of season one (Dexter chooses between well-adjusted and homicidal siblings) and season two (Dexter choose between well-adjusted and homicidal lovers), but as it turns out, that was only a secondary theme (as shown by the scene where Angel goes after his girlfriend's attacker and lawfully arrests him).
The primary theme of the third season was about overcoming the sins of the father. Not only does Dexter literally become a father with Rita, but he creates another killer in the form of Miguel just like Harry created Dexter. The potential for violence was there in both people--Harry just gave Dexter his code and Dexter just gave Miguel the knowledge how to kill. But in the end, Harry killed himself when he realized what he had created. Dexter killed what he created when he came to the same realization. The visions of Harry, then, though sometimes replacing what would be Dexter's narration for Harry's, serve a thematic purpose. This thematic thread is mirrored in Debra's character. Her relationship with a CI (Anton) is like her dad's relationship with his CI, Lara Moser. But, in the end, Deb could recuse herself from the case because of her personal investment (saving her relationship and her promotion). Harry couldn't recuse himself, leading to Lara Moser's death.
Now, comments about the season as a whole.
Masuka finally earned a role other than that as comic relief of dirty one liners and Mr. Exposition. He didn't have much more screentime than in the first two seasons, but it was much more varied screentime. Big improvement.
Camilla's return was welcome, and her death sad (but a long-time coming). It provided new insight into Dexter, and confirmed my long-held suspicion that she knew more than she was letting on.
Deb had interesting storylines in both her personal and professional life. She's poised to find out about Lara Moser, and by extension, Dexter's hidden past. But her comment that sisters are supposed to keep their brother's deep, dark secrets suggests this might not have the result we'd expect (perhaps veering the television series closer to the novels with her character).
LaGuerta's role wasn't as strong or as interesting as in previous seasons. I was concerned that Captain Matthews wasn't going to be in season three, but that seems to be a result of LaGuerta having such a limited presence. As stj complained, her past with the Prados didn't quite jive with her history with Doakes. Add to this a previously unseen friendship with Ellen Wolf, and her character seems to be wearing thin. On the other hand, her conversation with Dexter about secrets (and her willingness to secretly and illegally investigate Miguel Prado) offered new, worthwhile insights into her character. I disagree that the seeds of her finding out Dexter's secret were being placed down here, though. I read even less willingness to push things forward than stj in that regard.
I don't get the complaint about too little Rita, either. She was in plenty of this season (her kids, on the other hand, were barely in it at all). Early hints that the writers were grooming Astor to grow up a little quicker didn't go anywhere. I don't have a problem with the third husband thing, either. I don't see that becoming a plot point later on--the point about secrets has already been made.
Lastly, I was surprised by how many characters were retained for next season in the final episode. I was sure Anton would be out, but he's prime to return. Miguel Prado's wife is still Rita's friend and employer in the final scene, suggesting a return. And the replacement for Doakes, Quinn, will be back for another year (bumped up to regular status, I presume?).
As with the end of season two, I'm left wondering what can be done with the premise. But season three proved that there was plenty of life in it yet. I just hope they figure out something better to do with LaGuerta, and push forward Debra finding out about Dexter.