Well there are a few story lines still incomplete:
Trinity kills Rita. Dexter kills Trinity and disposes of Trinity. Dexter and Police find Rita, police determine Arthur Miller (Trinity) is on the lamb because he left his family. The Trinity case was officially given to the FBI, but this entire story line is dark now that the FBI doesnt have a manhunter. To the Kyle Butler lead is a matter of the FBI and obviously they wont find anything on Kyle or Arthur. So its just a wash. Maybe the blond from Cold Case can take care of it in 10 years.
So what happens to Aster and Cody? They just live with the grandparents while the legal custodian, Dexter, never talks to em again. Hell he preventative killed a pedophile to protect "his family" and now they are just out of the loop entirely.
Deb revealed to Dexter that Brian was his real brother (final episode 4th season). Now he knows, she knows, and his behavior doesnt change toward her (still distant). Better yet Deb doesnt see Dexter any differently. She doesnt have any intuition that Dexter has a darkness like Brian. Dexter is just neat, not controlling; he is withdrawn, just not damaged. Mon Dieu, how did she ever become a detective?
After sitting through season 2 and 3, they owe fans a little more than this. I would hate to have to wait till season 6 or 7 to get a cogent storyline that isnt filled with gaps and loose ends.
PS. The double homocide asphiciation masturbation murder! Why did the supposed sex fiends start in one warehouse and bleed all the way to the second for completion?!?