I can have a belated stab at some of these.

1. Yes, completely unrealistic. In any developed nation the parents and grandparents would be having social services knocking on their doors.
   
2. Seemed to be a sock or underpants surrounded by stains? Very strange scene but I think it was meant to be connected to the grandfathers friends apparently unpleasant toilet habits!
3. I think it was as you say, he chose not to make a wish that make others suffer. It is confused a bit by the father making weird remarks about the world being caring about music and stuff, but then at the end the father not knowing what was meant by the world.

As with some Japanese films some things can be lost in translation a bit, possibly for cultural reasons. But mostly, I just think this was a fairly average film. Like Father, Like Son is a far better offering by the same director, that was superb and didnt have the strangeness / lack of realism of this film.

6/10