What about pokemon itself? I mean even disregarding the concept of readily-available monsters that breathe fire and can control space/time that are given out to little kids on their 10th birthday...
Where's all the mass transportation? All the roads between various towns/cities seem to be unkempt, covered in grass, no place for any sort of trucks, and they're full of monsters, to boot. As for the few ships that exist, they tend to only run between two cities (and in all the cases there's no manufacturing facilities in either). Where do all the goods come from?
What sort of government is running? I mean pokecenters offer free health care for pokemon and trainers, free internet access, A/C, the works. One in each town, looking almost exactly alike. Nobody mentions bills or work, and people seem obligated to pay up a specific portion of their cash after losing a glorified cock-fight? Even the most remote areas seem to have a controlling pokemon center so there's gotta' be some major organization behind all this, but at no time does anybody mention politics or any form of government. Is it a hive-mind thing that just doesn't kick in until people grow older, so the kids are unaffected and parents send them off on adventures at 10, while they can still have fun, before their mind gets assimilated?
What do people and pokemon actually eat anyways? Some pokedex entries mention pokemon eating other pokemon (such as pidgeot catching magikarp) and that makes some sense, but some are generic and mention pokemon eating what we'd consider normal things, like "small bugs and worms". Does something have to be a certain size before it's considered a pokemon and therefore inedible to humans? Joltik's only 4 inches high, but IRL we sure as hell eat larger things than that on a daily basis. Hell, I take dumps larger than that!
Where are all the bathrooms anyways? People obviously eat (there's kitchens and restaurants in some towns/cities), but facilities seem rare, if they exist at all in a given region. Is everybody in pokemon a kryptonian with such an advanced metabolism they absorb everything ans so never need to take a dump?