One of my knocks against Dexter (in both the first 2 seasons) has been that the writers turn a really cool, thoughtful show into a "damsel in distress" scenario in the last quarter of the season. Those episodes overall are better than most dramas out there, but they still take away from the cleverness exhibited in the previous episodes.
Season three improved on that regard, but maybe only because that season was about the characters. "Freebo" is really a MacGuffin to introduce ADA Jimmy Smits (sorry, Miguel Prado). There's a murderer out there called "The Skinner", but he's not the true focus of the season like the Ice Truck Killer of season 1 or Dexter himself in season 2. Actually, the evaluation of Dexter's character began slowly in season 2, but picked up major steam here in season 3.
Season 4 is no different, even though we do have a villain to follow all season: The Trinity Killer. The writers seem to have found a much better balance of following a single case throughout the season while allowing Dexter to grow and discover who he really is (and also, who he wants to be). On all accounts, I'd say Season 4 is the crowning achievement and the best yet for Dexter.
There is still one knock, though. The writers of Dexter still have the tendancy to wrap everything up in a neat little package. The tiniest thing introduced earlier in the season has a reason for being - Debra probably didn't need to find out about Harry's CI's or the partial truth behind Dexter - I know that I didn't really care about that information being revealed to her at the end of the last episode.
Okay wait - another knock. After getting rid of an excellent character in James Doakes, they introduced Quinn. Quinn has been suspicious of Dexter all season long in #4, and it seems from the preview in season 5, that little bit is going to be ramped up big time. We've seen it before with Doakes, so I can only hope they're doing something original.
I will say one thing, though - the writers do a very competent job of wrapping up the season while leaving new questions for the next. It's gotten me excited in anticipation to see what they'll do with the character given what's happened at the end of season 4 (there are enough spoilers out there!).