-The monkey trio (moreso, Pansage). I just... wasn't a big fan, especially with Pansage I preferred Sear and Pour more. Then... one day I decided to get a Fukuoka exclusive plush (I love the store exclusives!) and decided to go with Pansage, because I didn't own any merch of him. I fell in complete love with that plush, and since then, I've loved Pansage!
-Tepig/Pignite. I really wasn't a fan of the piggies at first either^^ Tepig is cute in the anime (especially because 'Pokabu' is just an adorable name!) but I still wasn't a fan of him... And then I went to the Black and White Tour and the piggie just became more dear to me :) Pignite was in the same category. Then, I saw that the Kiosks started getting in his PokeCen plush. It looked awesome in the pics and when I finally got it, it became my favorite plush of the three secondary evos! His Jakks plush is such an adorable grumpig as well (more than the real Grumpig :p)
-Munchlax. Never a big fan of this Pokemon in general, but after getting ahold of his merch (especially my Tomy plush of him) he's grown to be an awesome addition to my collection! Like a mini Totoro :D
Alright, those are probably my biggest examples, and I'm sure I'm not the only one that's had similar situations :p