The fact that Lance's Gyarados knows Dragon Pulse in HG/SS (it's a Special move and Gyarados has crappy Special Attack).
Mine was that you can't teach Charizard Draco Meteor.
You can't capture Growlithe in Pokemon Blue, I REALLY wanted an Arcanine.
I always seem to get the least popular version.
Blue
Silver
Sapphire
Diamond
and possibly Black, unless I prefer the White mascot.
OT: You never know how overdesigned Yu-Gi-Oh is until you compare it to Pokemon.