Some of the standalone episodes occur with the child still missing and with many of the characters sort of ignoring that problem. There are unquestionably ways to do standalone episodes that wouldn't destroy this grand story—why can't they be tracking the child and end up in other places with problems—but Moffat and company opt not to go that route. It makes these standalone episodes that much harder to accept in a season which is crying out for more such episodes rather than less.
It is unclear how we, as an audience, are meant to accept the continuing of regular tales as Amy and Rory's child is missing – as a parent, would you sit idly by all summer, twiddling your thumbs, as someone else went to hunt for your child… someone you couldn't even contact? For some reason, Amy and Rory do exactly that, trusting the Doctor to make things right. It could be argued that the logic, maybe, is not wrong—he is the Doctor after all—but why they don't insist on going with him is a mystery.
In discussing this all with a friend, he succinctly stated that what the season lacks is "room to breathe." The weight of the larger story, and the number of episodes it appears in, crushes everything else. In an 18 or 20 episode season, the number of episodes (not the percentage) devoted to the story of The Silence, the plot to kill the Doctor, and Amy & Rory's child would work, but with only 13 episodes, it is simply too much. There are some great moments in this story, The Silence is an excellent new monster, and the child story is good as well, but it's all just too much.
Watched separately, the episodes which don't deal with this overarching story are sometimes very good, particularly "The Doctor's Wife," which was written by Neil Gaiman and "The Girl Who Waited" which reverses one of the stories of Smith's first season. In fact, these two episodes are shining moments not just of this season, but of the regenerated series as a whole. They show 
that Doctor Who isn't out of ideas for clever, wonderful stories, but rather perhaps just needs to rethink some of the more grand notions.
Not sticking too long on the positive, the basic way in which most of the episodes this season are structured becomes tedious as well. Rather than telling linear stories, this season is big on the "twist." Things do not simply progress here with the tension coming organically from the story itself. Instead, all too often the tension is derived from the story being told in non-linear fashion or with basic tenets of the episode/monster/problem turning out to be false (not that clues are ever provided for that being the case). While having some twist episodes is not a problem, when the audience starts to expect it of every episode, it becomes boring.
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