Metapod and Kakuna. Nothing's worst than fighting a Bug Catcher with all Metapods and Kakunas, and your Pokemon no longer have PP for their attack moves.
Zubat, I hate zubat! My last repel would always wear off 2 steps away from the exit of a cave and then I'd think "Oh, no problem just two steps and I'm out" Then I'd take 1 step forward and a wild Zubat would attack, I swear it had literally followed me just to attack at any possible moment.
for me, it's zubats and geodudes in kanto.
or pretty much any annoying cave dweller pokemon.
it's not so much bad fighting them, more then it is annoying just trying to get through the cave.
Any pokemon that showes up over and over again after you catch them. I we already have they ( unless you want to "catch" the opposit gender it is just sooo useless.) That is probly not an answer just throughing my two cents in. Pokemon I find annoying include: Magikarp( but is very powerful once evoled and lv.100) Bidoof,Wurmple and Cassacon