I was gonna answer the question with a question, saying "why are animals stronger than humans", but someone beat me to it.
We're just weak. Think about it. Here we are sitting in front of a computer typing about stuff that won't have any kind of significant affect in the universe now or in the future. All it's doing is making us weaker.
A lion, along with being build as a predator, does a lot of running and hunting and what not, which I'm sure builds its muscles and senses up. If humans didn't have the ingenuity to use tools, we'd all be stuck in a cave somewhere or dead, I dunno. The only reason most humans can even defeat a lion is because they'll shoot it with a rifle or stab it enough times in a weak spot. Very few of us, especially in this era, could do it with our hands, the ones that do are the exception and not the rule.
I'm not trying to be morbid or anything. I'm just saying that if Pokemon are based on animals anyway, it shouldn't come off as suprising that humans are weaker. In fact, you already have your answer if you consider real life first. Then just add on top of that the supernatural abilities and the fact that these monsters are usually larger than the animals they are visually related to and there you go.
Also, I don't think Pokemon exist for competition only, that's a pretty human centered way of viewing their usefulness in the world ("Horses were meant to be ridden!" Were they?), especially based on the "monster trainer" games. Pokemon Mystery Dungeon and the Hey You Pikachu games say otherwise, and even wild Pokemon in the "monster trainer" games are probably minding their own business.
