Here is my entry on how to deal with Mewtwo, coming from Raoga region.
"Oh Im just gonna use my Dragonite/Garchomp/Dusknoir/whatever to beat mewtwo, I got this"
Lol, you aint got no nothing guys. I keep hearing this around Raoga and I guess people are too shocked by the entire thing to be able to think clearly. You cant send bunch of (even strong) Pokemon against a full powered physical form of mind power such as Mewtwo , especially when we dont even understand how the entire Psychic type works. Im pretty sure he could make your Pokebros's head explode right away if he wanted. He probably doesnt tho, he has a problem with humans, not Pokemon.
Magic and science are strongly connected and both are weak and resistant to each other depending on how smart the users are.
So this is my plan. You cant just attack the source when the surroundings suffer. You have three elements in this huge mewtwo problem.
1. Mewtwo controlling Pokemon.
2. Clones attacking Pokemon.
3. Mewtwo dealing the final strike on its own.
First things first.
1. Web Of Disturbance.
Mind controlling can be easily put under control. Mewtwo is already easening on it since he's now going to attack personally, let alone that he cant control everything. Raoga has higly trained Psychic Pokemon such as Gardevoirs and Xatus, but we'll need Alakazams and some other Pokemon from the other regions as well. They all will create a strong psychic aura around the entire Yoko region. It will cause a huge disturbance and Mewtwo wont be able to control the Pokemon. We'll need hundreds of these Pokemo. Also, when you see the Alakazams, Xatus and other Pokemon randomly scattered around the region, they are not there randomly, they will be put there strategically and please dont distrub them, let alone catch them cos they are making the Web Of Disturbance.
2. Bats gone mad
Clones and controlled Pokemon are attacking everywhere. Do not, and I repeat and emphasize, do NOT try to attack them back or purposely hurt them unless you're in a need of defending yourself. They have no idea what they are doing. Even the clones. They THINK they share Mewtwo's goals, but as emphasized, they only THINK so. They all need to be disabled from attacking immediately. You think you are the only one who can be annoyed by Zubats? Guess again. Raoga and some other regions are crawling with Zubats (surprise surprise) and we'll have 10002s of them ready. All the regions will be divided into sections, each section having 1 or 2 Crobats, each of them being in charge of a colony of Zubats. One Zubat has a low chance of Hypnotizing a Pokemon, but a colony? 100% if not more. After every cloned/controlled Pokemon is hypnotized, a single Zubat will be patrol around them in case they wake up, hypnotizing them back. All the Crobats will cooperate with Pidgeots, Braviarys and other extremely fast bird Pokemon that will serve as strategy sources and communication centers, whether guided by trainers or not. my Braviary and Pidgeot will be leading all the Birds in Yoko region as they know all the parts of this plan and are strong enough. There will be a group of Gardevoirs in each region specialized for going into sleeping Pokemon dreams, curing them of their poisoned mind, one by one.
This strategy works for all the Pokemon, including the strongest ones.
To make this a lot easier, each region will also have a small web of Arcanines and if necessary, other fire Pokemon, using a heatwave on all the surroundings, weak enough not to hurt anyone, strong enough to make air warm and heavy to make Pokemon tired. it might affect all the Pokemon so stay inside houses as it's necessary to be done. Zubats will be followed by water Pokemon to help them stay fresh and rested. Yoku's Arcanine will be led by my Arcanine cos he's basically the best, and my Gyarados can follow the bigger group of Zubats cos he is the best just as well :D.
3. Dragon Pressure Circle
You cant expect to attack Mewtwo and get away with it, let alone win on your own. Its like battling a mew, just a lot angrier. You just dont do that, just like you dont go into a cave without repels or into a Victory road without a Pokemon knowing Strength, you eventually regret it lol. We need to get to him, but first we need to lower his psychic abilities. Dragonairs found in Raoga are extremely strong and willing to assist in order to keep the balance. "They control the weather", someone says. But in order to control the weather, you must control so much more than just "weather". A colony of Dragonairs will make a huge circle arround Mewtwo, surrounding him. They will use their abilities to make a very high pressure field around Mewtwo. A big group of Metagross', Gardevoirs, Espeons and similar Pokes will be aside, guarding the Dragonairs with all their power. their sole purpose will be to not let Mewtwo's attacks get to them. Dont worry about getting under his control cos with the Web Of Disturbance and Dragonair's Pressure Circle, it wont happen (99%). This will force Mewtwo to stand on the ground and stand on one place restfully. From here, someone will approach Mewtwo and explain to him that whatever he's doing wont help and that he cannot punish innocent people for whatever some idiots do to them. If he refuses to listen, Group of Hypnos will force him to sleep, Gardevoirs and Haunter will lock him into a sleep, being led by my Haunter and Umbreon (they're the very best, trust me), and he'll stay there till he comes to his mind through the TALK and TALK only. Hopefully we might even get some help from Celebi, Mew or whomever else is willing to help.
This is how science and magic work together. You can take this plan, change some parts if you wish, but follow most of it and save everyone, or disband it and see the region collapse while failingly trying to go against Mewtwo with whatever strong Pokemon you think might but wont work. Just let me know in advance so I can prepare some sandwiches and get the heck outta here.
Peace :D
Anyway, Im not usually into this kind of stuff, but I want points so I can get Pokemon I want, plus I finally have some free time. Anyway, this should cover everything, what we'd do in our region, what we'll do in Yoko, and how we will successfully battle Mewtwo.
Good luck!