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This design also makes sense to me. Much as the electricity in Chargestone Cave gave Klink its sentience, so too did the cold of that Unovan Freezer give Vanillite its sentience. Then again, I believe the lore says that Vanillite have been around for a long time, so I guess that’s not the case? So exactly why they’re around beats me. And I'd definitely like a clearer answer on that, because origin stories always fascinate me. But until then...asking why there’s sentient snow-cones is a lot like asking why there’s sentient sludge, and the answer for that is the same: because there just is. This is a weird wacky world with weird wacky creatures that form through weird wacky ways. That’s just how this world works. It’s happened all the time, and it will continue to keep happening. Good enough for me.
As far as the design itself, it’s clearly designed to be cute ice cream. And well...it’s ice cream. That looks cute. Vanillish looks a little weird, what with its blank stare and slightly deformed mouth. And Vanilluxe gets even weirder, looking like it tried to split into two but failing. Does this mean they reproduce by budding? Maybe.
Also notice that in the Gen VI moving sprites, this pokemon rocks back and forth progressively more slowly after every evolution. It's struggling more and more to move as it continues to evolve into increasingly unviable forms. What these sort of weird designs tell me is that, like Klink, these things aren’t supposed to exist. They formed through sheer accident, and are only continuing to exist through sheer dumb luck.
The theme here is that these Pokemon all look creepy and unnatural because they are creepy and unnatural. They don't look like they should exist because, as far as in-game lore goes, they shouldn't exist. And there are a lot of pokemon in the Pokemon Universe that are like this.
