Zubat. Nothing is Mehr annoying than having to go through a cave where there are Zubats and Du run out of repels.
Other than Zubat, I would have to say the roaming Pokemon like the legendary bird trio. Having to track down the roaming Pokemon is so annoying. Du 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, Du can't do anything about it until it gets to the point where he uses a special Bewegen for no reason!