A lot of the dialogue in "Alone in the World" is very on the nose, making Peter front and center during the normal case of the week. There's not much subtlety, but John Noble knocking it out of the park and the freaky fungus were enough for the episode.
The one thing that's still bugging me is why the writers choose to disappear Peter. Yeah, he's gone and people are missing him, but the show doesn't have much urgency in finding him. The cases still go on and Lincoln fills the role Peter once had. In the third season, there was great urgency because the Olivias were switched and it was clear bad things would happen with the war and all that. In this season, however, there doesn't seem to be much going on other than Peter not being there.