Ok I've finally watched the entire season over the last week or so. There are SPOILERS here, so if you don't want to read them skip this post.
I think this season was probably better than I anticipated. I had low expectations after watching the first two episodes. I liked how they dealt with the Dexter/Lumen relationship as it was nice to see Dexter in a relationship where the other person accepted him for what and who he was. What's weird is that I liked the Lumen character in spite of Julia Stiles somewhat wooden acting style.
I've always felt that the show's backbone was the Debra/Dexter relationship and this season was no difference. There was some very good scenes between the two actors throughout the year. The Jordan Chase character was a great villan this year. He had a really interesting character breakdown of Lumen/Dexter just before he got killed. I kinda liked Peter Weller's character I just wished they gave him a little more time to develop his arc a little more.
Now for some negatives: they should have written the Lumen departure a bit better. The way it was written in the episode finale was not really believable. I understand why they probably wrote her out (her contract probably only stipulated that she would be around for this year) but they should have done a better job of writing a more believable resolution. Well at least she still is alive unlike other guest stars.
Batista/LaGuerta pairing--I hated these two when they were together. I liked them as separate characters but when they are as a couple it seems like the writers just have to create tension/problems just to make the pairing interesting. Just have them split up already.
Quinn--how does this guy go from really zooming in on Dexter's activities to just dropping the entire thing when Liddy provided him with evidence. I don't like the way they softened his character throughout the year. Now they're setting up for Quinn/Dexter in S6 which is essentially a weaker version of Dexter/Doakes that was explored in S2.
Harry--these chats/hallucinations have lost all their interest because Harry never says anything interest or thought provoking anymore. He just parrots out obvious points and conclusions. The writers need to write better dialogue for him either that or just can the character because they are wasting the actor playing him.
Fuentes brothers arc--just seemed to disappear halfway through the year. There is still one brother alive, correct? They should have resolved this one way or another.
Astor--the actress playing her is pretty crappy. The less she is on the better.