This omission falls in line with speculation that Gooby is indeed an allegory for sexual molestation. When we were watching it, we immediately believed that Gooby was an actually an allegory for a boy coming to terms with his homosexuality.
First and foremost, when Gooby initially appears, Willy feels compelled to hide Gooby in the closet. The meaning behind this is patently obvious in this context.
Willy is always concerned that someone is going to find Gooby, or his secret repressed feelings. When Willy is trying to fit in with the popular kids, he can't take Gooby with him (besides the rated R movie sequence). If he exposes Gooby for what he is, Willy is afraid that he will be rejected by the popular crowd. Gooby spends this time alone, in a shed, far away from where he can be exposed.
Several quotes in the movie speak to Willy's struggle. When Gooby exposes himself in public, Willy pointedly says "What makes you think you could COME OUT?" Really?
Gooby encourages Willy to accept what is happening to him. Gooby suggests that they go on a "Voyage of discovery that will change [Willy] forever." A voyage to discover himself through his struggle perhaps?
The Dad also struggles to accept Gooby, but ultimately does. In fact, this may be his dad coming to terms with his with Willy's sexuality.
There are also a few crude visual cues of Willy contemplating his sexuality. During the soccer match, Willy is more than willing to take a ball to his face. At one point, Gooby scarfs down raw hotdogs like a champion! Dear lord, the kid's name is Willy!
There are some more quotes and whatnot that point toward this allegory, but, for the sake of some brevity, I have highlighted the major points. If anyone could stomach watching this again, I encourage you to view it in this context. The undertone of this movie becomes more than evident. I for one say good for Willy and his dad!
