First of all, what's going on with Atomos? Bahamut emerging from its Dalamud prison and trashing the place is all the Empire's doing, and it's all perfectly understandable. But Atomos? It just came out of nowhere and ATE our aetherites. Then it spawned purple-glowing monsters. The Empire doesn't seem to care. What the hell is going on with that? This ending did not bring any closure whatsoever to the whole Atomos issue.

Second, Bahamut destroyed a big part of the world and just settled down in a labyrinth? Really? Apparently, in ARR, the city of Gridania is even more beautiful and lively than it ever was, and the people don't seem the least bothered. It's like:

Bahamut: "Hey guys! It's me! I'm back. I'm still a bit mad at you humans for sealing me in a moon for so long, so I'll just vent out a little on you guys and destroy your homes, then I guess I'll build myself a maze and chill out and not bother you anymore, you OK with that?"
People: "Sure. 's cool, bro. We totally understand. Tell us when you're done and we'll start rebuilding. We could REALLY do some home improvement. You know, it's time we made new decorations and put a little colour in our city again. Shouldn't take more than 5 years or so. So long and thanks for the kickstart!"
Bahamut: "K, K. See ya. WOOOOSHFF-MEGAFLARE-".

Kind of makes you wonder why they had to seal it the first time. They could have just let it build its labyrinth, sheesh.