I actually like what they did with XY; as opposed to other games, they've made their respective evil organization, which would be Team Flare, not much of threat. Well, they were indeed a threat, but just weren't that emphasized. If they were in any other Pokémon game, they would've been dominating, and you would have been spending major time chasing after these guys.
As for which story-line I dislike, I'm not sure... I suppose I just don't dislike any. Although, I should still say that although BW2's plot was good, it just didn't have that great of an effect on me. Their prequels were fantastic, but when I played these two versions, it simply felt like a rehash, and not something new (which they were aiming for, I'm sure, but just weren't as successful in my eyes).