How did no one realize pokemon like the clefable line, the wifglytuff line, the togepi line, the gardivor line, etc was fairies until recent years? Why aren’t the skitty line and the blissey line fairies?

These two asks cover your first question, anonymous:

http://bills-pokedex.tumblr.com/post/149815193841/so-typings-are-interesting-before-the-fairy-type

http://bills-pokedex.tumblr.com/post/150152083081/i-do-sometimes-wonder-if-our-understanding-of

To put it in short, though, type classification is a complicated process, especially given how vastly different the physiologies of each member of a type actually is. This isn’t just taking into consideration secondary typings either (although, yes, things such as the fact that wigglytuff doesn’t respond to the fighting type the same way as gardevoir does due to one being fairy/normal and the other being fairy/psychic does make things a little more complicated). It’s also taking into consideration the actual, literal physical differences between the two. Taking wigglytuff and gardevoir for an example again, wigglytuff are a hardier species than the more physically fragile gardevoir, so even if both shared the exact same type configuration, figuring out that they are, in fact, the exact same type would require a keen enough eye on a researcher’s part to understand the difference between physical and elemental response. In other words, if a gardevoir and a wigglytuff were simply fairies (and not fairy with a secondary typing), if you punched such a gardevoir, it would bruise more than the wigglytuff, and it takes someone with particularly keen observational skills to know that this is because of physical frailty, not a weakness to the fighting element.

This all is to say that determining a pokémon’s type is a lot harder than many trainers know due to the interaction of different factors, and to do it because you had just found a type and need to go through hundreds of already discovered pokémon to see if there are any examples of that type in action is even harder. You can’t simply tell what a pokémon is at first glance, and there isn’t an interface that will tell you what moves are and aren’t super effective against a defending pokémon. You simply need to know what to look for, and sometimes, the signs are subtle.

As for your question concerning the skitty and chansey lines (blissey included), that’s actually an excellent example of what I was just saying at work. While it’s true that blissey can take a physical, fighting-type strike, the fact of the matter is that blissey reacts to the fighting element as a normal-type, not as a fairy-type. Likewise, skitty’s body reacts as a normal-type. Just because a pokémon is pink and/or cute doesn’t make it a fairy-type. For another example, jynx, which is thought to have witch-like powers, is not a fairy-type but rather a psychic, simply because she reacts to elements as a psychic would. It’s all about elemental reaction, not physical appearance, in short.