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