Perhaps I should clarify, not the story of the episode (though that had pacing problems) but the story of the arch itself, indeed the season so far felt as if it doesn't make a lick of sense.
Not a lick of sense? I don't know, it seemed to be pretty straightforward. The Doctor didn't want the Ponds to leave him, the Ponds were thinking about quitting anyway, and circumstances ultimately made the decision for them. That's the arc, isn't it? What's nonsensical about that? Or are you talking about something else?