The premise with pokemon is collecting them and that's about it. In all the games I've played, the plot is pretty shallow and consists of a kid starting out in a strange new world, discovering things and proving himself against gym leaders, and at some point in the middle you have the protagonist defeating a plot by some overtly evil criminals. Eventually he fights the very best and triumphs, and that's about it. Beyond battling other trainers and proving how wonderful you are, it's about trading and collecting as many pokemon as you can. The reason it gets away with it I think is that the original premise is quite an enjoyable one on its own merits, so no matter how shallow the tacked on plot is, it still works. Tbh, the plot is merely a vehicle for collecting and battling pokemon. There's an interesting bit in the first game when you find this abandoned building and through scraps of notes, you learn about the horrific creation of Mewtwo, but when it comes down to it, it's just another pokemon. Nobody expects it have a deep plot, they expect more pokemon to collect, battle and brag about. Sounds pretty shallow, but Nintendo have proved that latching on to a good idea and milking it for all its worth makes an awful lot of money, so I doubt they're going to stop soon.
