I have to disagree with your assessment of the movie. Mostly I disagree with this: "Mr. Incredible doesn't mind working with cohorts like Frozone and Elastigirl, but Incrediboy seems to be out of the running simply because he wasn't born with superpowers".
My objection is that you seem to think that Mr. Incredible denies Buddy's help simply because he has no powers. That is certainly how Buddy takes the rejection and moves the plot along, but I don't think that's what Mr. Incredible's objection was. First off, it's some strange kid that is obsessed with him (and from Mr. Incredible's point of view) is just another crazy fanboy. Also, Incredible's voiced objection is that he "works alone". And no where in the past do you ever see him working with someone! In fact he only coincidentally runs into others, but doesn't go off helping them, even when he's got nothing else to do.
Of course he then does go working with his kids and family later on in the movie, but again, it wasn't his choice to work with them. He also even voices his concern that the kids are there and in danger.
I think a better parallel to Rand's philosophy is that people (Syndrome) can become corrupt and overwhelmed with their power. Though from Bird's perspective, it doesn't seem to be inevitable.
To the counter-argument, I might further add: Mr Incredible even tries to stop his own wife from helping him fight the megabot at the very end of the movie - and she's a full-on superhero! It's not that Mr. Incredible hates people without super-powers, it's just that he doesn't want to put anyone else (super or not) in danger, ever. And therefore tries to discourage them from doing the dangerous things that he does. If there's something that he's guilty of, it's just sexism. Mr. Incredible accepts the help of Frozone because 'Fro is another adult male. It's women and children (super or not) that he refuses to work with.
On another note... hey man, maybe it's just a movie? Just entertainment? And not a philosophical statement about the proper direction of human society?