Why is that there are no trainers before the Main Character that beat Gyms, yet there are people with high leveled pokemon making it to the Elite 4? What food do people eat in the Pokemon world? Why is there no police in the Pokemon world? Why is the rum gone? Why don't gym leaders attempt to stop the "evil teams" in the region they are in? Why do people give you money after you beat them? How did Magnemite retroactively become steel type?
How is Kangaskhan born with a baby already? Why did the early Pokedex entries mention male Kangaskhans? Is the Nidoran line just one big line? Anything in the anime. How is it that no one else has found the legendaries in game? They're not exactly hiding very well. Why can't Scyther just innately cut down trees? How exactly does Sudowoodo block paths? Can't I just run past it?
"Wolverine is the Charizard of the Marvel world. Which isn't saying much." - darkdragongirl