Why is Togepi a rare Pokemon in Pokemon X & Y?

Question

Togepi isn't in the Kalos dex

Answer 1

Togepi is likely a rare Pokemon in Kalos because it's a rare Pokemon in general

Currently, Togepi is in 3 regional pokedexes, Johto, Hoenn and Sinnoh. Togepi can not even be obtained in Ruby Sapphire, and Emerald, so you might as well scratch Hoenn of the list. That's two out of six regions. That's pretty rare already. Now given, it is completely possible to obtain Togepi in other regions, like Kanto in FireRed or LeafGreen, but you only see Togepi in the wild in two instances, using the Pokeradar on Route 230 in Diamond and Pearl, and rarely in the White Forest in White. Outside of receiving eggs or in game trades, which there are quite a few of, Togepi is very, very rare in games, and even factoring in the former two methods of obtaining a Togepi, it remains rare. As such, it would seem logical that a Pokemon rare in the other five main series regions is rare in Kalos as well.

Hope this helps

Answer 2

Why is Wurmple missing? Why is Chansey missing? Why is Mankey missing?

Game Freak just decided not to include all previous 649 Pokemon in X & Y. That's all there is to it.

Answer 3

Togepi is available in the National Dex after beating the Elite 4, but it only appears in the Friend Safari Zone in Kiloude City. (It has received the new Fairy type, by the way.) That's why Togepi is considered Rare in X/Y.