About the B-plot of Real Life, Tom shows that the only way to live is to dive into the chaos (of real life.) The B-plot is a sort of antiparallel to the A-plot, in that the Doctor doesn't make Paris' choice naturally but has to be taught. It's technically two different plots, but one theme. I thought the sitcom nature of the scenario was perfectly absurd in any time other than US Fifties TV. Personal jeopardy to Tom had no resonance, as a star, he was guaranteed survival.
The absurd growing backwards premise of Innocence, which was low rated, was a metaphor for how we all face death as children. I think it would have been better if they came up with something that wasn't obviously nuts.
The A-plot of The Swarm was supposed to show that some enemy aggressions were too outrageous to go unopposed, even if violence was in the end justified. It failed, apparently because the insanely aggressive of blockading empty space didn't strike too many people as insanely aggressive. While it struck me as too impossible to take seriously. The B-plot was a hurt/comfort scenario (as I think they're called,) a very character driven story (in the most negative sense of the word.) Was it a soft reboot of the character? The initial version of the Doctor as having a terrible bedside manner certainly underwent a radical revision. Later, even when the Doctor was astonishingly egotistical, it was played for comic effect. I think the episode was supposed to be a sign post, so to speak, for the softening process.