The struggle with an Ultima story is it's going to feel like a cop-out if it's just 'Ultima's behind it all', because... well, we already killed Ultima. A while ago. With relatively little fanfare, with little idea she was important to this part, and in side content that they're (both most likely, and hopefully) not going to make mandatory.

So while she's definitely going to be relevant to any continuing story about this, she's not going to be the main thing, if for no other reason than the fact they aren't going to want to make both a Stormblood alliance raid and an Endwalker normal raid both mandatory.

...which yeah, as I mentioned in another thread, means that if this road's leading anywhere it's to Jenova.