Anybody using Blue?

I'll take these one at a time. :P

-Free animals are unhappy. Gotta catch them all!

You can say this about any animal in the real world. Wild cats and dogs are unhappy. Gotta catch them all!

-Animals in general don't need rooms, they can be stored in crampy spaced balls

They're not cramped. They turn the Pokemon into digital data to store them. The balls are essentially mini-hard drives.

-The boss of a megacorp is a bad person. Good persons are either scientists or arena masters, like roman emperors and Frankenstein.

What megacorp bosses in the series have been bad people? All of them have been friendly towards the heroes of each game.

-Nurses and Cops are cloned.

It's like twins, just on a larger scale. :P

-A mouse can be powered by lightning.

It's a fantasy game. Of course it can. It's not trying to be realistic at all.

-Give a shit about apprenticeship or college. You can live comfortable on the road and benefit from the kindness of strangers.

There's plenty of people in the series, both games and anime, that can't make a living on the road and freely admit it they couldn't make it as trainers. Likewise, there's plenty of people that do take on an apprenticeship or go to college and turn out just fine.

-A criminal is either a goof or a scientist.

Plenty of criminals in the series that are neither.

-Fish are stupid

Welcome to the real world. Most fish are stupid here, too.

-A flock of birds is dangerous and agressive. A single bird of the same type is friendly and helpful.

Wild animals can be dangerous, birds included. A single bird being friendly and helpful? Guess what, you can train birds to be helpful in the real world too!

-Stuttering the own name repeatedly is not a disability, its a way to communicate.

They're animals. Of course it's a way to communicate. Now, if humans were stuttering their own name, we'd have a problem.

-Powerchart: Mouse > Dragon > Plant > Bird > Caterpillar > Cat > Snake

I'm going to assume you're talking about Pikachu for the mouse. There's not a single dragon type Pokemon he would have an advantage over. Likewise, dragons resist grass type attacks, but don't have any real advantage over them. Flying types have the advantage over grass types, but you got the flying over bug right at least. Most cat pokemon are normal types, and bugs don't have an advantage over normal, likewise normal don't have an advantage over ANYTHING, so they don't really beat any of the snakes.

Care to continue?