Zubat. Nothing is meer annoying than having to go through a cave where there are Zubats and u run out of repels.
Other than Zubat, I would have to say the roaming pokémon like the legendary bird trio. Having to track down the roaming pokémon is so annoying. u can't even trap them with Mean Look since they'll always find a way to escape the battle.
As for the most annoying trainer pokémon, it's definitely Whitney's Miltank.
i'd say psyduck. he waddles around with a big-a** headache, u can't do anything about it until it gets to the point where he uses a special verplaats for no reason!