• Lack of Pikachu and its evolutionary family in 5th Gen. I really wanted to use one for my very first team, but alas...
• The anime after the original series.
• Those breeders in BW2.
• Lack of new Pokémon in X and Y. Granted, I love most of the ones we got, and the mega evolutions, but I believe that 6th Gen could have benefited GREATLY all around from another year in development. (Wouldn't have hurt to have 5th Gen in the spotlight for another year either.)
• All of the Kalos starters' final evolutions, particularly Delphox. Can't quite figure out why, but I haven't really warmed up to any of them. Perhaps, with Delphox, I was expecting a more stereotypical Western view on its witch design(with a pointed black hat and whatnot), rather than a mage design.
• No mega evolutions for Raichu, other starters or any Kalos Pokémon.
• The clothing on X and Y. Kind of nitpicky here, but I really think they could have done a lot more with the clothing options. Maybe some more unique pieces, but also items that could match other pieces more, I had a hard time finding a decent combination of blue and white items that I liked.
• Also, hats. Even more nitpicky, but I really wish you could take them off, or maybe have other head accessory choices.