I might have a couple of odd picks, but, firstly, Clefable. Specifically, its original 3D model. Especially, its shiny form. Something about that blank, inexpressive look on its face is so cute to me in a way that a smile couldn't be. The green on the ears, and lighter pink shade of the shiny just completes the cuteness for me.
Lopunny's Black and White 2 sprite just has a very graceful feel to me with the fluffy fur, and how it bounces. The huge ears, the boot-like fur near its feet, the stance that's like it's trying to stay warm, and little red nose are very cute to me. I also like the cute, sassy pose it does.
The original 3D model has made Salamence the cutest Pokemon, in my opinion. That kind of goofy face, the long tail that wags behind it, short limbs that somewhat hang from its body, and its slow glide-like way of flying are all just adorable to me. This model instantly makes me smile whenever I see it.
Ho-oh's reasons are similar Salamence's. The facial expression is somewhat goofy, for like of a better word, in a cute way. I just love how it flaps its wings, as well.
In her Ruby and Sapphire sprite, Chansey just looks so cute with how she has her stubby little arms on her egg, th tail visible behind her, and that tiny, happy smile.
In its original 3D model Minun just looks like it either wants a hug, or is cheering for you. That kind of blank smile that stays the same as it kind of bounces is adorable. It has a happy, peaceful vibe.
Espeon, in Gold, has a very serene look to it. The graceful, typical cat pose and inexpressive look, along with its big ears are just adorable. I just want to pet its head.
In Silver, it has curious expression, and the pose is somewhat sassy, which is also very cute.