Pokemon opens the imaginations of children to a world filled with joy and wonder. The joy of enslaving hundreds of intelligent, possibly sentient animals, and the wonder of personally controlling deadly monsters capable of destroying entire towns.
Consider Gyarados, Tyranitar, Charizard, and Groudon. All huge, all listed in their Pokedex information as capable of major property and environmental destruction. Each one having an important role in several competitive lineups. And you're expected to believe that these enormous monsters, capable of demolishing your fragile child-like body without effort, are going to sit down, shut up, and chill in a little red tennis ball until you let them out to fight. Additionally, they will follow all your orders, and never, ever will your slave monsters turn on you in a moment of repressed savagery.
Let's talk about one of my personal favorites, Scyther. It has swords for hands. Hold on, did you catch that? Let me repeat it. It has swords for hands. Awesome, right? Also, it can apparently chop through logs (size is never definitively stated) in a single blow. This is surely meant to sound impressive, but it really just raises more questions. How big a log? Lengthwise, or across? Hardwood or soft? The important thing to remember here, above all else, is that Scyther has swords for hands. This means no grasping at prey, no greeting a new employer with a handshake, no dancing with your owner like a Labrador Retriever. Of course, Scyther are bipedal, so I guess they can dance however they want to (Ha! Swords Dance!). To further complicate Scyther, it's a human-sized insect with a reptilian head. Your first thought may be "Why?!", but if it is, you're missing the point. This thing was designed for little boys. What is the coolest thing in the world when you're 8? Bugs. Possibly swords. Bugs with swords for arms? Priceless.
But for all his coolness, the fundamental question of "why are humans still alive" can't be answered by Scyther. He's a man-high, bipedal, twin-sword-wielding carnivore who is either coldblooded or clearblooded, depending on which part of his anatomy his circulatory system patterns itself after. Why he doesn't hack the impudent run who tries to capture him in half at the outset of battle is beyond me.
Which brings up my other point of contention. All of the Pokemon games make it sound like the world is incredibly dangerous, that you shouldn't leave your home village without a Pokemon bodyguard. Professors express shock that you would even consider setting foot outside town lines without a fire-breathing, water-squirting, leaf-blowing sidekick to make sure you don't get EATEN BY WILD POKEMON! Which is an event that, in my opinion, should have happened more often.
"You have found REMAINS OF A POKETRAINER!"
"You pick up ONE GOLD TOOTH!"
It's a real system shock when you go from "Don't leave the village or you will get violated by angry wild monsters" and "collect as many angry wild monsters as you can and wear them on your belt. This is your destiny". Call me crazy, but I don't know how comfortable I am with having Shredder "McSwords-for-hands" Scyther sitting on my belt.
The criminal organizations in the world of Pokemon are just as laughable as their massive murder monsters, with both regularly toppling to the whims of children. "Oh, so you're a rare and ancient manifestation of the power that created Lightning itself? How nice for you. Here comes a 9-year old with a red tennis ball. Guess you're nicked, chum." "Oh, so you're a massive, continent-spanning criminal enterprise with a plan in action that's been laid for years and involves cooperation and communication on a massive level? Here comes a 9-year old with a ball-covered belt. Game over. You guys can't handle this."
But the thing that breaks immersion the most....
THERE ARE NO BATHROOMS IN THE WORLD OF POKEMON. NONE WHATSOEVER. No wonder sewage takes on a monstrous form (Muk and Grimer) and wanders about... it's got nowhere else to go.