Retro Gamer'93, I never thought of that to be honest. I knew we actually had nukes but not that powerful. It's very probable that we would 'win' at the end but that's only after destroying the WHOLE surface of the Earth. I mean, such nukes would obliterate everything on the whole surface of the earth. However, I am pretty sure that some Pokemon, actually a lot, know how to use Dig, especially Ground types. So, wouldn't they just dig and hide low underneath the ground to protect themselves? They wouldn't last long enough down there without food or water but they could still trigger massive earthquakes from underneath so as to hit our underground bunkers.
Excuse me but I am only putting things in order. I'm not trying to convince that Pokemon would win. It's just that there is always something that Pokemon can do to counter a situation you bring up. For example, you say throw missiles at them.
Well, Psychic Pokemon can easily just stop those in mid-air and hurl them back at us. Only one powerful Psychic Pokemon like Gardevoir could stop many missiles and bullets all at once and just send them back. They could lift everything up and hurl it away. Lift tanks and throw them at us or blast them away or turn them into scrap metal.
Ghost types wouldn't even be affected by our guns. I suppose that ghost Pokemon have a solid and a 'ghostly' form so they can get hurt when solid but not when ghost form. So, the only way to hurt them is by sneaking at them - that's why Ghost is weak to Dark; they sneak and attack while Ghost Pokemon are in their solid form.
Steel types would also be nearly indestructible. Cloyster's shell is said to endure a bomb explosion.
And all of the others would be plain destructive. The 3 aforementioned would be the most dangerous. Ground and Rock Pokemon would be bad too. Psychic types could read our minds and act accordingly, use telepathy, sense our presence if we are hiding, brainwash us to kill each other or just stop attacking them, control our mind and create psychic barriers guarding them from assaults.
The thing is that you think of Pokemon as those cute and cuddly cartoonish things the anime shows. Here are some realistic pictures of Pokemon that kinda show how they would really be :
https://silver5.deviantart.com/gallery/31462640#/d41b32d
https://silver5.deviantart.com/gallery/31462640#/d3hs2lg
https://silver5.deviantart.com/gallery/31462640#/d3hs2lg
Also, watch some Heroes and X-Men. This can give you a good idea about how Pokemon would devastate the world. Furthermore just have in mind that in X-Men or Heroes there is only one person having a specific ability eg cryokinesis, telekinesis etc , yet it seems that a whole army can't put up with a team of 10 villains with those powers. Pokemon are a lot more. There are hundreds of Gardevoir not only one. Get my point?
I stress more about Pokemon because I don't think there is anything humans could do more than make a plan and start firing things to them. At the very end we may win with those nukes but we will destroy the whole earth.