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Brought Down to Normal - Everyone with supernatural powers, and even enhanced physical abilities to some extent, so as not to upstage the Pokémon.
Cast Herd - Traveling parties tend to stick together. People from the same canon tend to stick in traveling parties. The Soul Eater + Homestuck crew had formed an especially enormous Cast Herd that has all but singlehandedly populated Goldenrod City.
And they aren't even in Goldenrod yet. Imagine what just Azalea is going to be like when they make it.
Let's not forget some of the events. The nightmare event in September '10 and the MissingNo. event the following month. And then there was the time that Tarantulas unleashed a swarm of insane Bug-type Pokémon on Johto...
Lighter and Softer - As a counterpoint, the bright, colorful, Nobody Can Die setting provides quite a bit of light to characters from the more dark, cynical settings.
How about the recent event featuring soul stealing Shedinja?
Left the Background Music On - Played straight. It can't be turned off. It can't be blocked out. Nobody knows where it comes from. Occasionally causes character breakdowns. You'd crack too after hearing that cave music for a week.
It can, however, be drowned out by the radio.
It can also be drowned out with your own theme music, if you have enough badges.
Level Grinding - Pokémon can only gain a maximum of five levels per week, but considering how long characters stay in towns, this quickly adds up. It results in trainers with level 80 Pokémon challenging gym leaders with level 50 Pokémon.
Non-Player Character - There are a few of these, the most notable being Prof. Oak, gym leaders, and Team Rocket executives. Prof. Oak, however, takes it a step further in that he will not acknowledge anyone unless they specifically mention Pokémon — and then he goes off on a tangent about adventure.
Everyone should feel sorry for Officer Jerry. He will never have children. Ever.
"Mom" tends to freak out even the most hardened of characters.
Reality Ensues - The setting, while strictly following the rules of the game's universe, seems to take a fair amount of its flavor from the anime - routes are no longer a short jog but instead several days of walking to traverse, gym leaders are professional battlers who are to be feared and respected, and the thought of becoming a League Champion is a years-long ordeal.
The Scrappy: Youngster Joey has become an in-universe example.