1. What if they dig very deep underground? But okay, it may not be enough. Some human population could survive but some Pokemon could also too. Don't get me wrong again, but that's just my opinion. As soon as Pokemon sensed the shock wave from the explosion they would use Protect. Protect guards the user from anything. So they would survive that. Or Psychic Pokemon could produce strong psychic barriers. Now, most Pokemon would die afterwards from radioactivity but there are some Pokemon that wouldn't mind it. Pokemon with Magic Guard for example. Some Pokemon could tolerate it long enough so as to heal themselves and others as well with Aromatherapy and Heal Bell. Take Blissey. Humongous HP and Sp.Def means she would tolerate it and heal everyone with Aromatherapy.
2. There would only be one Psychic Pokemon. Look. There are 67 different Psychic Pokemon. Like animals, there would be thousands of each species. You can't just expect one Kadabra. Only one strong Psychic would be enough to control many missiles at a time. Duh! Two Baltoys alone managed to stop a space shuttle in mid air and those usually weight over 100 tons. Now let's do the maths. Baltoy has max 200 Sp.Att so doubled - they were two - and we go to 400. Thus, a Pokemon with 400 Sp.Att like Alakazam could control something as heavy as that alone. An Alakazam would control the missiles coming from the front and the Gothitelle next to him would take care of the bullets coming from behind.
3. From the whole passage you quoted, you only commented about Cloyster's shell pokedex entry. Okay, it's a pokedex entry. It may be exaggerating. But it could at least endure bullets. It looks quite sturdy to me. We aren't only talking about Cloyster though. Also, Ghosts could just float around us being invisible - yes most ghost types have this ability - and attack. Let alone that they could easily use Curse on a whole troop.
4. Toujours, most Psychic Pokemon are able to read the mind and thoughts of others, utilize telepathy, sense the presence of others around, create protective barriers. That's not me. It's Bulbapedia, Pokedex Entries etc
About telekinesis, I only have to tell you that they are Psychic Pokemon. That's actually what they do. They can control everything with their mind. If they couldn't they wouldn't be psychic. Only Unown and Wobbuffet don't do that. About brainwashing, well at least Lunatone can do it.
I agree that no every Pokemon would attack with the same power. But still, most of them have the same abilities, they just vary in intensity. An Alakazam could send 3 trucks flying with its mind at the same time, while a Spoink could only hurl away a car. An Alakazam could sense the presence of others hiding 5 miles away while a Claydol could only sense them if they are closer than 2 miles. A Gardevoir would be a better telepath than Grumpig. That's how it would vary.
Here is a line from Bulbapedia :
'It is said that Alakazam is known to have mastered every type and form of psychic ability, including, but not limited to: telekinesis, telepathy, ESP, psionic abilities, levitation, defensive techniques, mind control, and telekinetic blasts.' See? Alakazam knows how to mind control. Now, since mind control is just a different way to say 'brainwashing', we got 2 pokemon species that can control our mind. Alakazam and Lunatone.
5. Well, it may be fan art but it still shows a more realistic aspect of Pokemon. Golett is anyway cracked and ragged so that's how he would be in real life. How do you expect him to draw Golett if he is already ragged? Cute and smooth? I admit that the paintings show a darker side of Pokemon(like more goth style) but they are still good. At least you get an idea of how they would be. You may think 'a Galvantula doesn't look scary in the anime thus it can't kill me' but it would look intimidating in real life.