Yes, humans do eat Pokemon
In Episode 49 of the anime, Ash meets a Farfetch'd for the first time. Good old Dexter tells us the following bit of nightmare logic: "Farfetch'd, a Wild Duck Pokémon. Farfetch'd makes a delicious meal, especially when cooked with leek. Because of this, Farfetch'd is nearly extinct." Now, this is disturbing in its own right but think about it a bit further. We have just established that people eat Pokémon. We see other examples of this in later episode such as when Prof. Oak tells Ash that his freshly caught Krabby was too small to eat or when old lady Nastina talks about her hatred for Tentercools, coming to a point where she said "...you can't even eat them..."
The Pokemon games also points to humans eating Pokemon, particularly in Gold/Silver when Team Rockets cuts off the tail of Slowpokes and sell them to people to eat (for a million Pokerdollar no less).
Pokemon trainers are jerks
Did you ever found it chilling that trainers will ALWAYS force you to battle, whether you want to or not, no matter how injured your Pokémon are? Imagine: you're stumbling through a cave. Bats are attacking you left and right and you're forced to run from them. Your Pokémon are all injured; several of them are unconscious; maybe one's burned, another's poisoned. They're in no condition to fight, and you ran out of healing items. You just need to make it through the horrors of the cave and get to the next town where you can heal your buddies.
Then, a Hiker sees you. He shouts something ridiculous at you, like "I've been shouting all day, but I haven't heard an echo yet!" as he bounds over to you. Try as you might, you can't get away. You have no choice but to send out your injured Pokémon, which he gleefully defeats. Now you're alone and defenseless; the hiker grabs half your money and you crawl, injured and ragged, back to the last Pokémon Center, where you can heal your injured friends and then suffer the horrors of the cave once again. What the hell, trainers? Why won't you take no for an answer?
Pokemon and the real world
Think about this. In the Pokemon games, some of the Pokédex entries states that Poliwrath could swim across the Pacific Ocean and swim better than any human Olympic swimmer, Gastly can make an Indian elephant faint, and that Parasect's spores are used as medicine in China. Maybe this implies that the universe where the main series is set is the same as ours.
Following on the idea that the Pokémon world = real world: Imagine what they would *look* like in person, as photo realistic entities, with nothing separating you, from them. Say, for instance, you get trapped in an abandoned building with a number of pissed off Steel-types, Raticates, and maybe a ghost type or two. All of a sudden, you're living out a survival horror game if you don't have any Pokémon. This is to say nothing of what such monstrosities as Gyarados, Beedrill, Muk, Tyranitar, Nidoking, Pinsir, Ariados or god forbid Mewtwo would look like if one met them in full, photorealistic glory. Combine this with the downright terrifying entries and what you get is—BEHIND YOU
Pokemon as military weapons of war
In Pokémon: Lucario and the Mystery of Mew, the movie confirms a terrifying fact - in ancient times, Pokémon used to go to war with their human trainers/soldiers, who used them instead of weapons. Picture ghosts, psychic abominations, and things with awesome, inexplicable power. Now picture them at war, a far cry from normal Trainer battles, where Pokémon can't kill their opponent or attack trainers. The best death you can hope for is a Fighting-type snapping your neck like a dry twig. Consider also what little of Lt. Surge's background is given and the fact he is a LIEUTENANT, giving reason to assume that wars with Pokemon still happen in the present time.
Villainy of the Pokemon world
Ever notice the escalation of the villainy of the various teams? Team Rocket were generically nefarious, but mostly dim and restricted to ordinary organized crime. Team Aqua wanted to expand the oceans, which would have drowned coastal cities, and Team Magma wanted to expand the landmass, mostly by causing a volcanic eruption. These two were bad enough.
Team Galactic, on the other hand, wanted to SUMMON A MYTHICAL BEING TO DESTROY THE UNIVERSE. They wanted to end existence and create their own, supposedly "better" universe with Cyrus as the supreme ruler. In Platinum, Cyrus tells you he wants to unmake the world, and purge it of all traces of individuality, emotion, knowledge, and thought. And even after defeating him and pacifying Giratina, he tells you that he has not abandoned his plans, and will continue. He leaves you with this ominous line: "One day, you will awake in my world. A world without spirit."
Electrocuted? Burnt? Poisoned?
Pokémon are often fighting in battles for their trainers. However, have you ever thought about how those attacks really work? How the user performs them, and the amount of pain the opponent feels?
Consider these KO move. Having you limbs ripped apart by vicious pincers (Guillotine), being subjected to temperatures that would make liquid nitrogen seem like a steam bath in comparison (Sheer Cold), being drilled into and having your organs churned like butter (Horn Drill), and being hurled into a near-endless abyss (Fissure). Also, is anyone else disturbed by the fact that ANY Pokémon can learn Toxic? Think about what that implies... does the Pokémon... puke on their opponent... or maybe they-Ewww...
The source is actually not an article of any sort but more of a discussion portal to which I have lifted some things from and added my own.