I love Tentacool and Zubat (and their evolutions). They get so much hate as the common water route/cave encounters in the first few gens...there's just something endearing about them to me. And I'm not really a fan of Poison-types, either.
Not sure what the majority opinion is on this, but I really don't like Leafeon's design (or name). Yes, I realize its name is based on the Japanese name, but Botaneon or something would've fit with the other Eeveelutions much better (being clearly based on a type without being so...literal). It has an awkwardly large head and I don't like the ratty, torn leaves. I would've preferred more green on its body, too. Plus, those soulless brown eyes...
On another fourth gen topic: disliking Sinnoh is actually a pretty popular opinion, but my reasons for doing so probably differ than the majority; I think too many of the Pokémon have a dark blue color (and they aren't as colorful in general). Take a look at any sprite sheet with every monster, scroll through quickly, and you'll IMMEDIATELY be able to tell when you've hit fourth gen: "Lets make this one big and blue!"
Regarding the TCG, I hate first editions and reverse holos. Additionally, when I was younger (before the shadowless Base cards were really called such), I didn't like them. I called shadowless cards "'99 edition" (due to the copyright of ...99 Nintendo,Creatures), and shadowed cards "'98 edition" (...98 Nintendo, Creatures)...I traded a set of shadowless starters for a set of non-shadowless.