First, and foremost, would be Staravia with ENDEAVOR. I hate that friggin' Endeavor!!! Next would be Raticate with Super Fang (and at higher levels, Endeavor).
I don't find Diglett/Dugtrio to be that big of a deal. If you're battling in their territory, have the first in your party hold a Smoke Ball ... then say 'goodbye'!
Most annoying Pokemon to capture (aside from Legendaries), mostly definitely Beldum!!! You can't knock it down too low, or it knocks itself out with recoil, being it's only known move is Take Down. It has a catch rate of 3 ... same as the Legendaries. In 3 years of playing, I have only captured one. I figure it is MUCH easier to breed for another.