Gen 1: Charizard and Mewtwo. While I like Charizard, I don't think it deserves as much love as it gets. Venusaur and Blastoise deserve more love. And Mewtwo is overrated because it was the strongest Pokemon in RBY.
Gen 2: Typhlosion and Umbreon. Typhlosion just feels too much like a Charizard rip-off for me. And Umbreon just isn't really good, and doesn't deserve as much love as it gets.
Gen 3: Gardevoir. Many people love this thing because it's gorgeous. But in my opinion, Gardevoir is actually just an Alakazam wannabe.
Gen 4: Torterra, Electivire, and the Uber legends. Torterra just has too little going for it to deserve all the praise it gets. Venusaur is a strong, bulky monster, Sceptile is an awesome glass cannon, Serperior is a beast with Contrary, and Meganium is... cute. But what they have in common, is that they deserve more love than Torterra, IMO. Electivire has already been explained, and Electabuzz is better to me. As for the legends? They kinda got on my nerves years ago, just because they kept giving people a too easy time.
Gen 5: Emolga and Stunfisk. While I found Emolga cute at first, I grew to hate it because of Elesa, and because it disappointed me in Pokemon Conquest. Stunfisk, on the other hand, was a Pokemon I hated when I saw it for the first time. But while I grew to hate Emolga, my hate for Stunfisk decreased to just dislike. However, it annoyed me in Super Pokemon Rumble, and lately, I'm getting tired of the love it gets here. So, there is a chance that my hate for Stunfisk may return.