"Beauty is a characteristic of a person, place, object, or idea that provides a perceptual experience of pleasure, meaning, or satisfaction. Beauty is studied as part of aesthetics, sociology, social psychology, and culture. As a cultural creation, beauty has been extremely commercialized. An 'ideal beauty' is an entity which is admired, or possesses features widely attributed to beauty in a particular culture."
"The experience of 'beauty' often involves the interpretation of some entity as being in balance and harmony with nature, which may lead to feelings of attraction and emotional well-being. Because this is a subjective experience, it is often said that 'beauty is in the eye of the beholder'. In its most profound sense, beauty may engender a salient experience of positive reflection about the meaning of one's own existence. A 'object of beauty' is anything that resonates with personal meaning."
When deciding based upon these factors I first counted out things like cuteness which is commonly misunderstood to be the same; so unfortunately in my book Mew, Latias, and Jirachi are cute not beautiful because they resonate the feeling of child like peace.
Also due to it having to be female or genderless some Pok'emon I consider beautiful like Bellossom representing growth and life, Ninetales, and Glaceon do not count because they can be also male.
Based on this entirely too long of a rant my vote goes toward......Ho-oh, if you can not understand why I picked this and not an easy choice like Gardevoir or Milotic just look back to the episode of Ash's first day as a Poke'mon trainer.
After trials and tribulations coming against him to the point of possibly giving up his dreams the ray of hope emerges. The storm clouds are lifted after a display of sacrifice and friendship and a rainbow spans the sky with Ho-oh majestically flying by, shinning of a gold aura to showcase how special that moment is.
If you don't remember how beautiful this moment was just Google video this heading:
Pokemon 1st Episode- "Pokémon I Choose You!" (Part 3/3)