Is nobody going to mention Jolteon? Seriously. Screw that.
It always seems to have Double Team and, as someone who doesn't use Mind Reader, Lock-on and other such moves, that never goes well for me. I probably should use them, but I never really use low-accuracy moves - making them feel like more a waste of space than anything else.
Exactly the scenario that comes to mind. This was the worst. Had to tape my DS to my hand to ensure it didn't fly out the window.I think some of those who have battled the Kimono Girls in HGSS can vouch for you on that one. Double Team can just fudge off.
If it isn't for capture, one Pokémon I definitely dislike encountering is Zubat.
Zubat could be found in almost every single cave throughout Kanto, Johto, and Hoenn, and they could be quite deadly; their encounter rate seems to be sort of high, and when your Pokémon is under-leveled, causing you to be unable to escape, they would snatch up on the opportunity to use moves like Supersonic, which would confuse you, leading you to get hurt and whatnot. It's sort of bothersome. Same applies for Golbat.
Another is Tentacool. This one is like Zubat in many ways, but it resides in sea for most part. We run into it pretty often, and it has tendency to utilize Supersonic a lot. Alongside, it's also got access to Poison Stick (which it isn't afraid to use), and it does have a good portion of chance to cause your Pokémon to become poisoned.
Anything with Sturdy. I'm sorry but no matter what your lv. 13 Geodude shouldn't be able to survive a 4x water attack from my lv. 70+ water type.. Roggenrolas were an especially big pain in B/W and B/W2.
Pelippers were also the bane of my existence in R/S/E. q_q I remember being so annoyed as a kid each time I fought one since they used Protect on their first turn 95% of the time and that was no fun, not when you're training your team. You're going to faint anyway, don't delay it. Siiigh.
Gliscor. Gliscor is literally Hitler. I actually love his design, but he is the devil.