@ Giratina hates Shaymin : Okay if a teenage is brave enough to approach a 'little blob' and kick it in the face then okay he wins.And I mean even a cat or a small dog can survive several kicks and punches,especially Happiny who has the life force of 5 elephants(looks at her hp..crazy for such a 'little blob')..Fear comes to play.Pokemon wouldn't fear us since they would be something like aliens and like every other movie aliens invade and kill fearlessly.We would be even scared to approach a togepi since it would be something strange and you never know what it could do to you.Anyway Happiny is very powerful from a range.If she comes to close combat with a teenage then okay she is gonna die if she doesn't do something.But still she can protect herself and heal with Wish and Protect.And if she is some meters away then she can lift whatever she wants,cars,rocks etc and throw them at us turning us into flesh and blood.
Also,bullets don't necessarily equal to death since even an elephant needs 35 shots from an elephant gun to die.Now imagine how many shots a cloyster(resists bombs as well),steelix and generally every steel,rock and any other bulky pokemon like blissey or hippowdon would need.
And I really think that all Psychic types,so as to be able to be psychic and use their mind power,they need to be very intelligent.There are others as well like Lapras etc.And they don't need to be smart they need to be strong physically or mentally.
Also about the rarity of Pokemon.It's not us that would go to their planet and so we wouldn't find them because they would be scattered in various places away from each other.ALL the Pokemon would concentrate and invade us,so expect some thousands metagross to come as well.Only 1 metagross could do the job(read some pokedex entries) now imagine 500000 of them.
And finally,from the 6 billions humans only some millions,if so,are trained to help in a war like this.So 1 million humans vs billioooons of Pokemon.Yeah we would win.
And don't forget that we only have guns,bombs and mines.
Well they have their counterparts.Bullet seed is exactly like a gun,bombs=seed bomb,magnet bomb and mines=stealth rock,spikes,toxic spikes(they are not explosive but they are still hazards)..Now as someone else said imagine a skarmory setting us all these and whirlwind us around.Painful isn't?