Most of the misfit toys do not have any problems with them:
A cowboy riding an ostrich would be a cool toy.
All Charlie-In-The-Box has to do is change his name
A polka-dotted elephant would be an acceptable stuffed animal, and such toys are sold even more frequently than in the film's release.
The squirt gun that shoots jelly just needs to replace its ammo (or, alternately it would be an awesome breakfast toy).
The Dolly had nothing wrong with her except for her own depression, which could be helped simply by being given to a loving family.
The boat that can't stay afloat probably isn't meant to float; there are plenty of toy boats meant to be played with on solid surfaces, such as the USS Flagg.
Others only had minor problems, such as the train with one set of square wheels or the swimming bird (which is not that weird, as there are several birds that are aquatic), that Santa could easily fix. That's the point. Just because they are misfits doesn't mean that they are bad, which, by the way, is the aesop of the whole movie.
The full cut shows that Yukon Cornelius kept licking his pickaxe because he was prospecting for peppermint, and found it at the very end. Most people would think that mining for anything in the Arctic Circle would be crazy (since there is no tectonic plate up there that would contain minerals), especially when it is not something that you mine in the first place. That means that, like Hermey and Rudolf, Cornelius was a misfit that was vindicated in the end. It would also give relevance to why Cornelius is about the only adult who isn't a pompous, antagonistic jerk to the two at first.
Going further, Yukon's sled team is made up of misfit dogs—not only are none of them the typical breeds that pull sleds, they're all of different breeds. They were probably all strays that Yukon found in his travels that no one else wanted.
Notice the Head Elf's voice changes when he's talking to Santa before "We Are Santa's Elves." He usually sounds intimidating, but he sounds more calm and has a higher pitched voice. He's kissing up to Santa since he's his boss, of course he wouldn't sound threatening talking to him. The moral: Better to have a brown nose than a red one.
The Elves contempt for Hermey makes more sense from the perspective he doesn't want to make gifts for darling little kids in favour of becoming a dentist. Saying he doesn't want to make little kids happy can be taken the wrong way easily enough, but to want instead a job that in the cliche cartoon world is often feared and associated with pain by children really digs himself in deeper.
Comet isn't pulling the sleigh on Christmas Eve. Santa took him out for the way he treated Rudolph.
In the end credits, the elves are dropping off the Misfit Toys to new homes. One elf picks out the Bird, takes a look at him, and the umbrellas he's been giving to the other toys, puts the umbrella away, and tosses the Bird down. And then you remember the Bird was a misfit because it couldn't fly. That's assuming, of course, that Santa didn't fix that for him.
It has wings and may be able to glide down, it just couldn't get into the air under its own power.
In the scene, the Bird is seen actually flying, so apparently, he somehow developed the ability to fly. Also, the Bird never says he can not fly, only that he does not fly, he swims, so it could refer to a personality quirk (unsurprising as many of the Misfit Toys problems are psychological or involve nonconformity in a conformist world).
The Misfit Toys are supposedly just toys that were unloved that ended up on the island — but think about it. At the end when they are shown being re-delivered to the kids, they don't really fix up any of the toys' problems (elephant having spots, or train having square wheels, for instance) — so, it's possible that the toys will just end up on the island again.
It is stated expressly that Santa can find for the toys those children who will actually love them as they are.
Everyone is a complete Jerkass to Rudolph because of his nose, and this is never dealt with—at least in the song, anyway—they only accept him because it turns out to be useful. So it leaves one wondering about what would happen to a child with a real disability.
This is probably why, in the famous holiday special, his parents show remorse over how they treated Rudolph even before he has helped rescue his family, and when he returns, Santa Claus immediately apologizes to him before he has revealed the power his nose has over the winter visibility.
So Santa gets to judge the morality of all the world's children, but he turns a blind eye when it comes to his own reindeer?
I think the point is more that even Santa can make this mistake, so no one else has any right to claim to be too good to need to learn it. Also, Santa's realization of his own thoughtlessness fits the show's theme of redemption and that even Santa can benefit from it (rather than sit on his laurels).
The treatment of the Bumble. He appears to be just a wild animal, and behaves like one. Nothing he does is malicious, he only goes after characters because he's a hungry beast trying to survive. And yet they treat him like a villain, and even have an uneducated dental enthusiast rip his teeth out without anesthetic.
Although to be fair he was unconscious when his teeth were ripped out.
Remember this first aired at a time when declawing housecats was fairly common.
If Rudolph's nose was bright enough to cut through fog, then wouldn't that hurt everyone's eyes? Perhaps that is part of the reason why the other reindeer excluded him from their games?
The misfit toys lived on the island for a presumably long time, and possibly set up extensive relationships and culture while living there. When the toys are delivered by Santa, it is very possible that these toys will never meet again.
Even more bittersweet if one considers the aforementioned possibility that these toys will be sent back to the island.
There's something that always bothered me with the "Chewing dolls" line. Sure, after the special came out there were chewing Cabbage Patch Kids dolls (See the Funny section), but what about Nutcrackers? A classic holiday symbol! That's if you count them as dolls, that is.
No parent would let a small child play with a nutcracker! Trust me, you don't want to spend much time imagining why not...