Patrick

No, they’re just rarer now.

This is so discouraging, ok =/

It's discouraging that you have to look a bit longer for a Totodile?

That's a terrible way to be looking at it, you need to understand that some things need to be rarer to have a sense of achievement when you actually find/catch them. Without rarity differences on specific Pokémon then everything has the same value and makes trade/auctions very dull as well as making the game very easy to complete the Pokédex.