So, we met the Silents. Cool idea, especially with all that "Silence (or Silents) will fall" stuff that went around. The way that phrase was bandied about, I thought it sounded like a bad thing. What I hoped it meant by the end of Day of the Moon was that, as nasty and evil as the Silents were, getting rid of them actually caused a big huge problem. Maybe while they were amoral, the things they were doing were actually important and necessary on a Earthwide or universal scale. Or unleashed something far worse.
We also had some stuff in the first episode that didn't pay off in the way I thought. Amy and River both reacted to the presence of the Silents in the same way, with odd twinges in their bellies. We now know it was because River was Amy's baby, but I thought it may well have been because River was also pregnant. With that thought in mind, I wondered if the little girl at the end of Moon was in fact River's daughter rather than Amy's.
I also wondered about Rory for the whole season. At the end of Impossible Astronaut we have Rory with Silents behind him. The lighting effects when they swapped back to River suggested the Silents were starting their electrical energy blast thingy, and were going to shoot Rory.
Next episode all that and the girl in the spacesuit was completely ignored. I kept waiting for an end of season reveal to what had happened, but no. I seriously thought that maybe Rory had been replaced, and then we got the Ganger story. At the end of that story, the Doctor gets Rory to step away from Amy before he turns her into gloop, and I wondered if that was so Rory wouldn't get melted down as well.
When we got to Good Man Goes to War, I thought Rory would be the good man of the title. To some degree, there's nothing to contradict this, but they make it fairly obvious it's meant to be the Doctor.
Let's Kill Hitler got me excited in the potential for an Evil River to be the main baddie for the rest of the season, if not for her being bad into the next season. They blew that out of the water by the end though.
So, those were some of my thoughts on what may have been going to happen. As you can see I was completely wrong every step of the way. One thought I had from very early last season was that Moffatt was going to start to distance the Doctor from the whole Time Lord/God thing that Russell Davies set up. That said, I knew it would have to be a gradual thing because it was so much a part of the Tennant Doctor's run. So far I've seen hints that returning the Doctor to his unknown wanderer roots is slowly happening, we'll just have to wait and see how that pans out.