I've only started playing the game recently, and so far I've gotten to the "challenges" mission in the Jungle Relic area. Out of what I've played so far, the hardest mission for me was the one where you had to get rid of all the Grimers and the Muk in the Fall City sewers. My capture styler broke at least five times against a group of three Grimers. I somehow managed to get the Grimer/Muk group on my first try, though.
The latest Pokemon I captured, Flygon, was a real pain as well. It moved so fast, I barely had time to get a few loops around it. And since I couldn't really use Plusle's discharge against a Pokemon like Flygon, I was stuck doing it with no Pokemon Assists whatsoever. I don't really want to know how difficult Salamence is going to be...