(in fact, it almost seemed to be deliberately dystopic, with Molly's reactions to Daphne and Matt calling her "your mother," unless it was just poorly realised

I think it was meant to be mildly dystopic, that they could have been happy if the world weren't tearing them apartment with Daphne's job and how many disasters there are because of the powers.

The only question is - will powerless Peter be more crazy, or less?

I would think more, since he no longer has justification for thinking the things he does.