Fast type.
Seriously. He is specifically focused on Pokemon that can move fast and hit hard. Defensive Pokemon with big overwhelming moves are always the ones he has the most trouble with. It's also why he had so much trouble training Grotle/Torterra.
Sure, there are outliers each season like Snorlax, Bayleef, Corphish, the aforementioned Torterra, Palpitoad, and Goodra, but even then most of those got the least amount of screentime, with the exception of Bayleef which was probably only written in because it was the director's new fetish.
He also sucks with most ranged attacks.
Energy Ball, Draco Meteor, Electro Ball...that encompasses some of the only ranged attacks that aren't entirely element-based (Thunderbolt, Bubblebeam/Water Gun, Ember/Flamethrower, Ice Beam, Leaf Storm, you get the point) that he's had (besides Water Shuriken, which works Because Greninja™). All three of those posed challenges for his Pokemon to master. And he always has difficulty with ranged attacks in battles, too. Unless his Pokemon dodges it, which is whenever the writers don't feel like jobbing.
It just so happens that three Pokemon that fit this type of battling style in Gen 6 are part-Flying, so he had three Flying types in Kalos.
