I half wonder if there aren’t a few additional elements to this.  Like, it seems that most, if not all, Pokemon are intelligent enough to know that humans are far more “defenseless” than the average Pokemon is.  

I mean, sure, you have those Pokemon who are extremely territorial/aggressive/hungry, but at the same time not all Pokemon are like that.  In fact, I would say that most Pokemon tend to want to avoid conflict at all, unless it somehow extensively threatens their own life in some perceived way.  And even then, most attacks directed at humans seem to be more along the lines of a small warning (when Pokemon threaten other Pokemon, they tend to get the a more forceful attack).  A researcher with rotten luck is an exception, apparently. 

Then again, perhaps I’m just being overly optimistic by saying that Pokemon are less likely to attack a human than they are other Pokemon by virtue of their realization that the human would never survive a few thunderbolts to the head. As I mentioned before, if you have a Pokemon that’s angry or hungry enough, they aren’t going to seem too concerned over human fragility.   

Add to this the chance of friendship; as Bill mentioned briefly, many people choose to form some kind of pact with Pokemon to help raise/train them to grow stronger. Perhaps most, if not all, wild Pokemon recognize the potential to become stronger by teaming up with humans, and so have a vested interest in not killing them all. 

… . Or we could all just be deluding ourselves and the real reason Pokemon haven’t aggressively hunted humans to extinction is simply because all of them have tried eating us once and think we taste exceptionally awful. 

If you can’t eat them, join them. 

— @anonabsolxwolf​

It’s also very true that pokémon frequently see us as friends, which is why newly captured pokémon tend to take being tamed so well. There are also instances of pokémon quite literally choosing their trainers due to any number of positive qualities that human may possess. Researchers have no doubt that pokémon are capable of being vastly intelligent, although how intelligent may depend on the species. (Alakazam, dragonite, and metagross are thought to be far more intelligent than even humans, but slowpoke … generally are not.) Nonetheless, the fact of the matter is, what you’re saying about pokémon sapience and their drive to form bonds with us is certainly true, and I thank you for adding that.

On a similar note, it is also certainly true that human meat does not, in any way, appeal to anything that one would think would eat us. This is also why animals generally don’t make the attempt. Seeing as I, for one, am not a cannibal, I couldn’t imagine what about our meat is so unappealing, but yes, this is why we are not on the food chain to anyone unless there is quite literally nothing else to eat.

…Except wherever our life forces are concerned. Ghost-types are quite fond of that, unfortunately.

—Bill