He's startled by the question, as if surprised she would even ask him that.

"Oh, I couldn't name a favorite, I love them all! That's why I research them, after all." Although.... "I suppose Poison-types have a special affection for me, but that's just because not many people are fond of them, so they respond especially well to love and affection."

So yes, while he wouldn't call them his 'favorite', he's careful to go out of his way to give the unloved Pokemon extra love.