I thought the story was great. Sure, it wasn't as exciting as Reborn, but it is still better your average Pokémon game.
The thing that did bothered me with the story, was how so many people had access to a legendary Pokémon. I understand that the reason for it is to give you a bit more difficulty when it comes to defeat a NPC that has a legendary on their team. I just felt that it was a big too much. Usually, an "important" NPC would have 6 pokémon, one being a legendary, another being a mega-evolution and/or delta Pokémon. Showing off the different "types" of Pokémon is great and all, but the legendaries lost some of their sparkle that makes them special. They are called legendaries for a reason.
Also, another thing was how one NPC said "The legendaries doesn't agree with what the person, that they are following, wants to do to the world". Then WHY in the world do they follow these people?! Darkrai was seen leaving the leader of the Darkrai cult without any problem what so ever. It's not like the legendaries are forced to join the powerless humans.