WMG / Rio

Plot

Blu was brought in to mate with Jewel in order to tame Jewel

Keeping an anti-social bird alone will not make her more social. She may have even killed other birds herself before this film began. Blu was, in theory, a way to get her to trust humans since he was non-aggressive, of her species, and trusted humans perfectly.

They were left unsupervised specifically so Blu's owner did not know just how dangerous Jewel was.

• Uh, Blu was bought in to mate with Jewel because they are the last of their kind. Did you miss that or something?
  • The OP's idea, I believe, is that it's a cover story.

Marcel and his goons weren't arrested for wildlife contraband.

They were arrested for disrupting the Sugar Loaf cable car. And the samba school parade with their chicken float. Of course, once there, Fernando's testimony nailed their contraband operation for good.

Nigel had a hallucination during the Pretty Bird

Pretty Bird is pretty much different from the whole movie and even from other songs with all these backgrounds, lights, TV, newspaper, globe, etc. The whole song except the end is shown by Nigel’s perspective. Then the perspective changes back to Blu and Jewel’s… and everything is normal again, it’s just a dark dirty room full of cages with the dim light from the window. So maybe Nigel had a hallucination because of that chloroform rag or just because he is insane.

Characters

Nigel the evil Cockatoo is actually Snowball past his prime.

He's quite used to being in the spotlight, but all fads fade with time. Cockatoos in general just love to be the center of attention... losing it would easily be enough to turn one bad!

Marcel is Fernando's Dad

It was never explained why Fernando is homeless, but it's sad, nevertheless.

Theory: Fernando was the child of Marcel, but the mother died after the child was born. Marcel may have given up Fernando, which is why he's homeless.

The real kicker is the line where mentioned that Fernando reminded Marcel of his childhood.

Jewel killed the last Blue Macaw born in the wild before the movie

• Jossed by the sequel.

Nigel is an immortal cockatoo.

He had a near-death experience in the middle of the movie, which got him off our heroes' tails for a while, as well as the near-death experience near the end.

In the sequel, Roberto will hit Nigel's Berserk Button

Nigel can't stand the idea that any bird could possibly be prettier than him. And given the fact that Roberto is pretty much the bird equivalent of a grade-A Bishōnen... well, you can see where this will go.

In an extreme case, Nigel will either try (and possibly succeed) to make Roberto "ugly" (likely in an excruciatingly horrible way) or just kill him. If he succeeds at either of these, it will likely invoke an Alas, Poor Scrappy reaction, in and out of universe.

• Jossed. During the movie, Nigel's focus is solely on Blu and doesn't harbor as much resentment to all the other "pretty birds" from before including being around other Spix's Macaws.

Nico wears a bottlecap as a hat, because he was a pet

Canaries aren’t native for Brazil. Also, there is a line in Hot Wings: “I’ve been around the world and I wanna live my life in Rio”. It is doubtful that Nico was able to do it himself, so maybe he was travelling with his owners, and then something happened to them or Nico was lost. And now he uses the bottlecap because he is closer to humans than any other wild birds in the movie.

Settings

The Blue Macaw species is still doomed

Because there is only one pair of this species in the entire world before the finale, and other blue macaws are directly descended from them. In the long run, the birds produced from a single pair would suffer from far too many genetic defects and would be too vulnerable to disease. It's only buying time. There is also necessary Squick.

• In real life, the birds that Blu and Jewel are based on (Spix's Macaws) are being bred in captivity in zoos in different parts of the world, most notably Al Wabra Wildlife Preservation in Qatar, which has the most. Who knows? Maybe one of the chicks they've bred will be sent to Brazil in the future (or at least in the Rio-verse).
• The sequel shows that there are, in fact, more Blue Macaws around, in the Amazon, so jossed.

There are other female Blue Macaws.

And they will get into the mating pool.

• Sort of confirmed in the sequel. There are other Blue Macaws, but they're not in the mating pool.

Rio and Madagascar takes place in the same universe

Do I really need to explain?

Rio and Ferdinand take place in the same universe.

That's not even a theory, this is canon, since we see in the latter movie newspaper with news of Linda and Tulio discovering Spix macaws in Amazon.

Meta

Nigel was originally supposed to die in the airplane rotor

This movie originally had a PG rating and changes were needed to get the G rating. Since it's not implied at all he survived and it's tacked on at the end, it seems having him survive may have been one of the changes.

Maybe he would have died at a very early point in development.

• Maybe they decided to keep him alive not because of the film's rating, but because they predicted that he's going to become an Ensemble Dark Horse who needs to return in a potential sequel (which he did).

Disney shut down Blue Sky Studios as revenge for stealing the idea and leading to the cancellation of Newt

Rio and Newt both involve two animals of the same species, opposite genders, and opposite personalities being put together for the purposes of repopulating their species.

• Jossed, as it has been since debunked Rio was never at fault for Newt being cancelled, but only story issues that was plaguing the development which then cancelled Newt entirely and turned into Inside Out.