I've noticed a trend in children's movies that has been happening for a while, but only just came to the point of severe irritation. I'm talking of the tendency to make social misfits into the hero.
Finding Nemo did it. Nemo had a malformed fin. Happy Feet did it. Mumble had a malformed head and vocal chords (thanks to a negligent father, I might add, as if there weren't already enough stereotypes). Tale of Despereaux was about a mouse who didn't know how to be a mouse, e.g. was not afraid of cats and didn't like cheese. This hearkens back to the days of Dumbo, the floppy-eared elephant whose drunken pink elephant sequence still gives me nightmares.
I know the main character has to be different to those around them, or they won't stand out, but how far and how often does it have to come to this? Hiccup in How to Train Your Dragon was a Viking misfit. Bolt was a bit stupid, but, really, he was just Buzz Lightyear in disguise. Remy in Ratatouille is definitely a social misfit. So is Linguine, for that matter.
I suppose this is slightly easier to put up with in live action because they tend to stick to stereotypes we understand. Sam in the Transformers movie is a social misfit, but he's a nerd, so we accept it. Bruce Willis' character in Surrogates becomes a social misfit through circumstance, so we accept it. Dave in Kick Ass is a social misfit because he dresses up in a suit and tries to help people, but in this case he's the only good person in a world of grey, and it's quite sweet, so we accept it.
But come to live action again from another angle, and people with disabilities were historically represented as evil. Now I would say they're not represented at all.
I know the hero has to be different. They have to be someone who can work as a change agent, to bring about a new world order, and to have the courage to think the thoughts that no one else can. That doesn't mean they need a physical deformity to show their mental difference, even to children.
And, of course, the issue with anthropomorphic animals (Mumble has a built-in bow tie in his feathers, for goodness' sake!) is a whole 'nother post.