Mega Mawile and regular Mawile, Arcanine, Meowstic, Noivern and Talonflame,
While Mawile is underrated due it's absurt damage output, it still became one of my favourites, no idea why I guess, maybe some things can't be explained. When I discovered Mawile gets a Mega Evolution I was happy for the first time that someone got a well deserved evolution, and in the end Mega Mawile became one of my main Pokémons on Pokémon X.
I discovered my love for Arcanine pretty late. He always supported me in almost every Pokémon game and done well even till this day; it may be a old timer but he sure packs a punch.
Meowstic, the first I time I saw her I thought it was going to be a useless cute-y looking Pokémon with no real purpose. Good thing I was wrong about that, it's becoming a great asset to my Pokémon Y team so far and the whole design and stuff just grew on me when the time flies by.
I thought Noivern was going to be another zubat clone at first, buy holy bingo skippyballs he is amazing in terms of speed and power, and it's evolution line is pretty solid.
Talonflame would be the most underrated Pokémon I judged I thought it was going be some useless flying type due the lack of movepools that he was going to be underpowered and stuff, but that's not the case at all. Even thought I almost use him as a suicide-destruct Pokémon with Flareblitz and Brave Bird spam. I still liked him in the end. (Yes, I learned how to roost him now properly don't chew me out please. :<)