I always thought Bobby was Mikey's alterego

That's an interesting perception. I can tell you based off what the director said though that everything is suppose to be taken literally. I would prefer a movie that instills a sense of ambiguity into the viewer.

What do you mean she never acknowledge Bobby. She does throughout the movie. Remember when Bobby says mom I love you and she says I love you too or when she's putting them in the tuband tries to remove Bobby's clothes.Or what about the end where she is asking where's Bobby?