Why is it Dave/Octavius Brine can talk to humans when no animal has been able to as established in the first movie? Cephalopods, ESPECIALLY Octopi have been noted to have an intellect that can sometimes rival even humans, so it comes as no surprise that one could learn the human tongue.
Actually he has a special mic with a human/octopus switch, according to his needs.
Also, he's an octopus, his beak is actually below his head where it belongs, but he can fake a human face. His teeth are just graphic. He can make himself look entirely like a human when he wants.
Why was the serum that mutated the penguins called the Medusa Serum? Well, consider the results of the serum and then the legend behind Medusa.
The Ho Yay between Private and Rico near the beginning of the film makes sense seeing as penguins are one of the animals most reported to have homosexual members.
Also, the penguins consider each other brothers, so the Ho Yay wouldn't even register between them anyway.
The theme of the film is about wanting to be important and valued. Dave became evil because he resented the fact that every zoo he went to, he was overshadowed by penguins and he plans to turn every penguin in the world into a monster in order to get his revenge on them for taking away his importance. Private's main conflict is that he resents the fact he is not treated as a valued member of the team and the penguins as a whole feel that they are not valued by the North Wind. They all feel that it is their right to be considered important and valued. By the end, Private is accepted as a valued member of the team due to perseverance, bravery and doing what's right, the penguins get accepted by the North Wind due to their single-handedly stopping Dave while Dave gets Hoist by His Own Petard and is defeated by the device that he made in order to get his revenge. The message at the end is "You do have a right to be respected and valued; but it's a right you have to earn".
Why does Dave seem to not care that people might realize that "Octavius Brine" might be responsible for the monster-penguin outbreak? He's shown shapeshifting into Octavius, it's likely that after this plan he can simply change his appearance again and assume a new name.
Why are the 'professional' spies so dismissive of the penguins? Because they're all predators, whereas the penguins are all prey!
That is actually relative. Penguins, while prey to large predators like leopard seals and orcas, are also predators to fish. Meanwhile harp seals are also prey to polar bears. However, one can still say wolves and polar bears are higher in the food chain than penguins are.
The adorable little squid that Skipper interrogates in Shanghai? He was probably sold afterwards and eaten.
During their escape from the plane, the penguins crash through the roof of a plane, harass it's pilot then opens an airlock and clips the tip of the wing. If you know about aviation disasters, planes have had fatalities (if not outright crashes) for much less.