Rio/WMG

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!

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.

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 not know just how dangerous Jewel was.

Nigel was originally supposed to die in the airplane rotor
This movie originally had a PG rating an changes were needed to get the G. Since its not implied at all he survived and its tacked on at the end, it seems having him survive may have been one of the changes.
 * Jossed: The rating change was because of some edgy gags.
 * Maybe he would have died at a very early point in development?

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.

Marcel is Fernando's Dad
It was never explained why Fernando is homeless, but it's sad, nevertheless. This troper believes that Fernando was the child of Marcel, but the mother died after the child was born. This troper's unsure, but Marcel may have given up Fernando, hence why he's homeless. The real kicker is the line where mentioned that Fernando reminded Marcel of his childhood.
 * This troper saw it more like Marcel complimenting Fernando in order to encourage him to keep working there. He probably has other kids working for him, and I imagine he treats them all the same. There are lots of homeless children who make a living out of contraband on Rio's favelas. Fernando's parents were probably killed in a fight between contrabandists and the police.

There are other female Blue Macaws.
And they will get into the mating pool.

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.