I'm pretty sure i can make a list for each generation:
Gen 1: Starmie. I know, i know. Starmie is a great pokemon, and perhaps on of the most iconic from the first gen via its association with Misty. I think that's why i never liked it, because Misty was possibly the hardest gym leader i faced when i first started pokemon as a kid (started with charmander). Yet, when i finally started using Starmie competitively in the 4th gen i started to respect it a lot more. Plus, i just love the red gem it has. The color scheme is great on that pokemon.
Gen 2: Probably Skarmory. Can't really give a reason other than the design of the pokemon has grown on me. I've never been one for stand-alone pokemon, but this one has steadily started to stand out from the rest of the stand alones out of Johto.
Gen 3: No-brainer on this one. Breloom. If you went back in time to when Ruby/Sapphire/Emerald were current i probably wouldn't even remember Breloom. Well, sort of..I mean it's not like Spinda / Maractus / one of those other pokemon that you struggle to remember because they aren't that significant, but it just didn't stand out to me. It getting technician probably changed my view on Breloom. As you might guess from reading my aforementioned text, i focus on the pokemon's design to a certain degree, and i will admit i didn't like it at first. I will say now, that i do in fact love Breloom's little beret-helmet on his head.
Gen 4: Rotom. Loathed the base form design. Still do. Mainly dislike the lightning bolts on both sides of it. The release of the extra forms, mainly the Lawnmower form changed my attitude towards Rotom.
Gen 5: Pretty set in stone with how i feel about this generation. I despise the starters of this generation with the exception of Samurott, but i sort of went from dislike to more of an accepting view of Emboar when i saw his shiny form. I just feel like the blue flames on him work out better and compliment his design more.
Gen 6: Ok so this change was fairly recent. First, a story. As a Louisiana resident, Mardi Gras is a time-honored tradition and staple of my life. One of the best parts of Mardi Gras is going down to New Orleans for the Mask market. My favorite type of mask is without a doubt the Venitian masks popularized by plague doctors in the 17th century. I just love the beaks, as they make for a very eye-catching mask. Coming back to Pokemon, i recently picked up where i left off on Pokemon X and Y, and when i finally caught spritzee (which i had originally viewed as girly and strange looking) i reexamined it and it just seems like it has the same characteristics of a plague doctor mask on it. Basically, i've made a complete 180 in regards to spritzee. Although, i definitely plan on taking on a spritzee shiny grind as i like the purple spritz over the pink.