Finding Nemo/WMG

Dory spent some time in an aquarium.
As Gill points out, and as Nemo's time in the tank shows, fish in aquariums tend to go insane. Dory lived in an aquarium, probably a large one, and that is how she learned to read.

It was a large public aquarium, and they had dolphins or small whales; that is how she knows how to speak whale. They also had sharks (what large aquarium wouldn't?), and so she doesn't have the instinctive fear of sharks that normal fish have.

Naturally, she doesn't remember because her time in the aquarium damaged her memory. She especially doesn't remember ever being in the aquarium.
 * "Short-term memory loss. Mm-hmm, it runs in my family. At least, I think it does... where are they?"
 * It would also explain how she understand how to read English. She must have spent some time with humans to be able to read.

The species of fish and other underwater life evolved from a common ancestor who lived in/around the shores of America.
This is why nearly everyone speaks in American accents.

The Tank Gang gets out of their bags, only to die of ocean-born pathogens.
Gurgle could've seen it coming: With their environment filtered and closely monitored, they would have no real immunity to germs and parasites also living in the ocean.
 * Nope. The end credits show them playing in the ocean, perfectly fine.

The Tank Gang escape the bags because of Nigel
His beak should be strong enough to tear through the bags.

Bubbles is doomed the first time he encounters a little blue penguin.
Penguins leave streams of bubbles to confuse predators, but if it attracts dinner...

Nemo's Mum is his Dad.
The dominant fish in any clownfish shoal becomes female, all others stay male. Nemo's Dad is the only adult clownfish in the locale, therefore he should be a she.

Coral (Nemo's Mom) is still alive, but she suffered Laser-Guided Amnesia (the classic kind, not the kind Dory has)
There was no blood in the water after the Baracuda-scene.
 * Maybe because a Baracuda is large enough to swallow a clownfish on the whole.

Large parts of the film never happened.
'Nemo' means no-one. Maybe Nemo doesn't exist.
 * Then why does Marlin leave his anemone?
 * Delusional. Duh.
 * Alternatively, Nemo was killed in the beginning along with Marlin's wife. Marlin fell into a psychosis, and the entire adventure is purely imagined.
 * So would Dory be his subconscious trying to let him know everything but her (or at least her amnesia) was an illusion?

Dory is actually Coral, Marlin's Wife
Coral never actually died, she just was severely injured from the barricuda attack. She stop breathing for a little bit, causing brain damage (erasing her memory and making her inable to encode new memories) and causing her skin to turn permanently turn blue. She was found by a family of blue tangs and they helped nurse her back to health. When she sees Marlin, she still can't really remember her old life with him because of the trauma from the attack, but she does still unconsciously feel a connection between them. Yes, I know this makes zero sense, but hey, Wild Mass Guessing, it doesn't have to.
 * No I like it
 * What about decidely non-clownfish features like the bigger size and the shape of the fins?

Marlin was tank-bred.
He's fearful of the outside world. He doesn't understand the way the ocean works, besides sharks and everything bigger than him eating fish. That's just instinct, and instinct is impossible to breed away.