@DeepImpact: ...All pokemon powers are natural abilities. Also...
Pokemon: "We are conveniently crippled in exactly the right way to make us less awesome so the underdog can beat us!"
Humans: "Sweet! This is not forced at all!"
Reminds me of that time Star Wars decided to make enemies both lightsaber and force immune. Do you see the problem? The deus ex machina isn't even remotely subtle, meaning suspension of disbelief dies, in an explosion.
If I might make a recommendation, making humans stronger causes a lot less problems than making pokemon weaker.