Well, I am admittedly kind of jaded about the video game industry in general, so maybe at least relative to modern warfare #347, pokémon is a better game. It's just it would be so easy for them to make the game way better, if they weren't a bunch of misanthropic money grubbing megalomaniacs.
1) pokémon learn more than 4 moves
2) you can dodge trainers
3) less random encounters, especially in caves
4) More than 44 bytes per pokemon so you can give them actual depth and uniqueness.
5) No PC, but the day care is accessible before you beat the whole goddamn game
6) Stories besides "evil org tries to destroy world, you hit them until they stop."
7) Branching dialog
8) Changing landscape. (Why has no game ever let us burn down the Burned Tower?)
9) Costumes that change the overworld sprite.
10) Ally NPCs. Later games sort of sort
of do this.
11) Breaking your own stereotypes to shake things up. Rival befriends you, no doctor Oak, pic related, evil team are the good guys. The cave turns out to be a town instead of fucking crobats everywhere.