The XY story was beyond moronic, impossible to take seriously on any level. Like Mega Evolution and Z-Moves, it's something someone might come up with to make fun of the franchise. "Epic in scope" isn't a good thing if it's impossible (or nearly impossible, since apparently you did) to buy into the story. GF's failure to realize that (though they did much better with SM) is one of the worst things about their approach.
It's flawed, sure, but despite that it does actually do a good job of going into background story on stuff like Mega Evolutions and AZ. And while it isn't quite on the level of destructuon Cyrus's plan would have if he were successful, The fact that Lysander wanted to commit genocide seemed a bit more malicious in scope. (Maybe it was the fact that the ultimate weapon was powered by the souls of helpless Pokemon.)
No, the story did want to tell grand things and had the components to do so. I personally think it did partially deliver on what it wanted to do. However it did have some issues that kept it from sticking the landing. Perhaps if the pacing was more eveb, it would have been better.
That said, I will admit that there is one other aspect of XY that could be clouding my judgement: The fact that I went in mostly blind since the release happened worldwide. Sure I knew about all the new Pokemon, but outside of officially revealed stuff about the Gym Leaders and the few story bits, I had no idea what was coming. It was the first time since, well ever really, that I didn't know about most of the game prior to getting it. Heck, I did a better job avoiding spoilers for XY than I did for SM. (Stupid Youtube.) So the fact that there were things about the plot that took me by surprise (again, Lysander was prepared to commit genocide to save the world) probably reflects a bit better in my eyes.