Jynx, of course, creeps me out.
What really weirds me out is Croagunk mostly for its in-game cry especially when its anticipation ability makes it shudder. It makes me think of the twisted kind of shudder.
I would have to say, Froslass. It's a skull in a kimono. *shiver* On a side note, I find it a little odd that when a wild Onix or Steelix use Dragon Breath, it comes from their pelvis. I don't want thatkind of breath on my pokemon.
Design-wise, Alolan Golem, Aromatisse, Mega Alakazam, Gurdurr, Magmortar, Probopass, Magmar and Lickitung are hideous and I can't see them for more than 10 seconds.
Lore-wise, I think Drifloon and Palossand crossed the line by making playgrounds and beaches unsafe places. And the fact that the latter has an artwork of it murdering a Pikachu makes things even worse.
Beedril, I already hate bees and wasps in real life and my fear is always shown whenever I see one. Now let's just say, make them roughly the size of a child, that alone would terrify me. Oh and it gets worse once it Mega Evolves, not only it gets more stingers, it also becomes a lot more aggressive. So yeah, I do have an irrational fear of wasps, hornets, yellow jackets and yes, even bees, though bumble bees are okay as they keep their distance and bees without stingers are okay as well. But any bug with a butt needle is a bug I'm not okay with.
-Drowzee and Hypno. Even before I found out about the creepy child abduction things. Those are the faces of people you don't trust even when the sun's out.
-I will always find Marrowak sort of creepy. The first introduction to the pokemon in the main games is THE ANGRY GHOST OF A DEAD ONE that is so full of rage (from how I've always seen it anyways) that it's riled up all the ghost types in the pokemon tower to the point you can't identify their forms right away and the ghosts are possessing the shrine maidens that tend the tower's graves.
-Igglybuff. WHY ARE ITS EYES RED WHEN IT'S EVOLVED FORMS HAVE BLUER EYES?? Its eyes want to steal my soul.
-Xatu has always given me Aztec/Mayan vibes. And that reminds me of my childhood fears around the Mayan Calendar and the end of the world. Even if I don't buy into that stuff anymore seeing Xatu still gives me spine crinkles.
-Girafarig's second head. Brr.
-Solrock's eyes creep me out so much. It looks so sour and judgmental. But if it wasn't squinting all the time they'd just be tiny red dots inside a massive black void and that is somehow worse.
-Drapion's long neck and head arms creep me out. I get that the head arms are supposed to be its pedipalps but the design just don't translate that well for me.
-Musharna's fine. Until it opens its eyes. If she'd kept munna's eye style she'd be fine but JESUS DON'T OPEN THEM NO
-Zygarde and all it's forms. If I lived in the pokemon universe and stumbled upon it in a cave I was exploring I would pray to every pokegod that would listen that it didn't see me. It just feels so wrong. Even moreso than ultra beasts do.
-Take away Shiinotic's mouth TAKE AWAY ITS MOUTH
-Meltan and Melmetal. I can't see them as anything but ditto who've absorbed liquid metal and have a big black staring orb that both looks like and doesn't look like an eye. It's just like... someone took out the pupil of an eye and suspended it in the middle of a giant nut. The creep factor is easier to see on Melmetal since part of the nut it's housed in is cut off by the body and doesn't create a full white circle around it. And Melmetal comes to be by feeding a Meltan 400 'candies' you get from turning in 400 meltan to the Go professor. I CAN ONLY SEE MELTAN CONSUMING ITS BRETHREN.