Just some story points just didn't really keep my attention, or feel as well developed as previous seasons. This one seemed very John-centric. Meg didn't really feature much at all. Detective Franco (if that's his name - aka Angel from Dexter) didn't really follow up any more on his suspicions of John's involvement with Danny's death. This was one of the main points of tension in the last season, and it just seemed to be dropped after Marco's murder. I think they should have kept that thread running the whole way through.
There was very little with John's children. We hear that the girl is starting to mess about with some boyfriend, but we don't get to meet him, or see what extra stress that situation would put on John.
Nolan seemed to appear pretty suddenly, and didn't seem to have any of the troublemaking capabilities he did in the last season. He just kinda sided with the O'Bannons at the trial, there was nothing really about his having to choose between the Rayburn family, and his dad's best friend. There was no mention of his mother really at all.
We didn't hear what happened to Roy Gilbert, whether he was dead or had just discharged himself and disappeared to escape the heat.
Ozzy turning in to some kind of prophet was kind of weird.
We didn't get to hear anything else about Robert Rayburn's alleged affair from previous seasons. I thought that might have been explored a little more, though maybe it was something that was planned for the future.