I actually think XY has a nice skeleton of a story. The whole past war thing, AZ's thousand-year-redemption-story, Xerneas/Yveltal being used as weapons, Lysandre being the most dangerous villain yet, Malva being the Holocaster and an E4, etc. There's a lot of good ideas there, the game just seems to be afraid of touching these things because of criticism they got to BW, a very story oriented game.
A 3rd version could flesh out in a way that it could be up there with BW and SM, bring Zygarde to the story with the whole Ragnarok thing, develop Team Flare more and how much they control Kalos' society, give us a better background for Lysandre and how he became so twisted, touch up on his relationship with Sycamore and Diantha (maybe show make parallels between them and the Serena/Calem/Shauna/Trevor/Tierno), let the gym leaders actually do stuff, etc. But lol rip all that potential.
Lack of a decent story really hurts how a game is remembered. I bet very few remember how good the credits song is with the neat multilanguage lyrics, but that's what happens when you're there fighting AZ at the end of the game and you barely cared about this world and its characters.