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When choosing a favorite shiny it is hard because there are so many cool ones haha. But Gigalith is my favorite shiny due to how awesome his colors are.
I'm annoyed at how Gamefreak treated Shiny Pokémon; they introduce the concept with a Shiny Gyarados, which looks SO different (and so awesome) in comparison to it's standard colouring. And then, for so many other Shiny Pokémon, they're merely a slightly different shade to their regular colouring:
(to be fair Squirtle's shell is green but otherwise he's the same)
And, of course, there's the unnecessary love of neon-green:
(Note that the three examples are from Generation II alone!)
However, in the case of some others, the changes are at least significant enough for me to be able to appreciate them, such as the afformentioned (and unfortunately common) Gyarados (and there are some others I like, of course):
Shiny Rapidash is cool indeed, but shiny Ponyta is better imo.
My favorites are probably Cryogonal and Sneasel though. Dem chains and dat pink/yellow.
Here are some others I kinda like:
Spoiler:
I noticed something. Gen 1 has a love for neon green. Gen 2 has a love for pink. Gen 3 has a love for autumn brown/orange. And I seem to have a love for blue shinies, haha.
Rayquaza is awesome as a shiny... Well now that I think about it both Kyogre and Groudon are both awesome as shinys as well... I think legendaries get so love by gf. They try to make them good as shinys. Ho-oh and Lugia are awesome too. Non legends though I like Swampert and Scrafty
I think it should be obvious who my favorite shiny is, given my current posting theme. Nidoking is my favorite Pokemon, and when I found out his shiny form is blue (one of my favorite colors), it was just perfect. I still haven't caught a shiny Nidoking in the games. Some day.
I've always like shiny Pokemon that really differ from their normal color schemes. Some of the first that come to mind that I really like are Azumarill, Magikarp, Rapidash, Ninetales, Dragonite, Lucario and Rayquaza. There are dozens more that are pretty good, too, but I hate when they look like the first few that giradialkia pointed out, where they're just a slight change in shade.
Some of my favourite shiny Pokemon include: Ludicolo, Shuckle, Mothim, Seismitoad, Heatmor, Gigalith and Bravairy. I suppose if you look at it, I'm quite a fan of those with a good splash of blue. 8)