One of the biggest problems in the Pokemon universe is that there is tall grass everywhere, and no one is mowing it. Maybe it wouldn't be such an issue if electric rats, fire dogs, and hypnotizing sloths weren't hiding out in it and attacking children at random; a pretty massive landscaping flaw. Of course, the process of actually mowing the grass would require a huge amount of effort at this point. Plus you would need lawnmowers capable of grinding through creatures made of pure rock and steel.
Sure, there are trade routes. And the tiny, isolated towns seem to be well-stocked in the essentials: It's not like anyone's dying of the measles or starving to death. But for some reason, the first town you come into contact with only has regular Pokeballs. No Superballs, or Ultraballs, or any of the better balls. They exist, and are being mass-produced. Why not ship a couple to the town surrounded by rattatas and pidgeys? You could probably make a fortune off of those small-town rubes. Instead, they're stuck with regular Pokeballs and regular potions. Now, if only they'd start mass producing Masterballs, maybe half my team wouldn't have to die to catch Mewtwo because I wasted the only one in existence on a Psyduck.
3. City Planning
Who the hell designs these cities? Why would the only way to get to a certain road be by cutting down a bush or traipsing through a house? Why are there cliffs that are totally impassable from one side? Get your shit together, Poketowns.
4. Animal Shelter
Maybe there wouldn't be feral Pokemon roaming aimlessly through the countryside, blindly attacking everything they see, if there was a place for untamed Pokemon to go. Animal shelters! A staff could take care of them, and find them homes where they wouldn't have to fight to the death to prove their worth; lest they get stored in a goddamn computer like a forgotten Macy Gray mp3.
5. Child Welfare
Kids have it terrible in Pokemon world. The first trainer you play as lives in a 40 square foot town of three houses with no store to buy food, no school, and no hospital. Also, he hasn't heard of Pokemon, which is pretty much the only thing the rest of the world ever talks about. Then he goes out on his own fighting monsters for an old guy and his mom couldn't care less. She checks in occasionally, but shouldn't someone be concerned that a 10 year-old kid isn't going to school, but is instead fighting dragons and ghosts? That he's completely on his own, and traveling by foot no less? That he's battling a terrorist organization single-handedly? Mommas, don't let your babies grow up to be Pokemon trainers.
6. The Internet
Computers exist in the world of Pokemon. So does the internet, apparently. But for some reason, it's not our internet. On our internet, whenever anything is discovered by anyone, it is forever logged a thousand times in the untold trillions of sites. But no such Wikipedia exists in Pokemon to document all existing Pokemon species, so that people don't have to rely on an amateur, inexperienced child trainer to go figure this shit out for everyone. Hell, in every generation they find out that there are about 100 more Pokemon they never even realized existed. Either there is some crazy genetic experiments going on, or Pokemon world just needs to learn to communicate a little.