I'm fine with Fandaniel taking over Zodiark. Fandaniel's shtick was that he didn't want the rejoining, he wanted to kill. Fitting for the final villain, all that was left was explore "why". Honestly I kinda of expected him to take over Zodiark since we've been dealing with ascian body-robbing a lot again in SHB, I imagine they were doing that so Zodiark being taken by Fandaniel didn't feel like jumping the shark. Sadly the expansion went and jumped the shark anyway.

Theory: maybe executive meddling, or something else, changed the plot mid development. Their original idea was to kill Zodiark on the moon as the big climax.

Zodiark's trial is so much more dense compared to the other ones. Hydaelyn is just a copy of Shiva and the Endsinger has like, one mechanic. Zodiark however is very dense both mechanically and thematically. Also, he doesn't have an ultimate move. I imagine that what they had wasn't usable for a trial that early so they just cut it out.

The terrible pacing is a classic example of a plot that's been chopped and rearranged. We're here, then we're there, we do this and then that, all without feeling a natural progression. The whole moon thing; we got there via a random teleporter... remember how much the moon was hyped up in Shadowbringers and before? Or hell, the logo of Endwalker itself. Perfect for a FFIV style ending where the big ship makes its way to the moon to kill the threat there. However, instead there's the whole exodus plot that doesn't concludes into anything, feels empty and pointless and raises more questions than it answers (for example, certainly Meteion's dynamis gun would be able to aim for whatever planet we fled to, right?).

I've made multiple posts criticizing Meteion, I wouldn't be surprised if it was Meteion's inclusion that made the story feel like a lego build of plot devices. After all we can't have two ultimate bosses. Zodiark shouldn't be able to defeat this ultimate villain if we are to fight her, so we introduce a new metaphysical mechanic (dynamis) and reduce the previous ultimate evil into a macguffin.

I don't know. The whole thing rubbed me off the wrong way since two days after the expansion launch, when I was clearing the later half, in particular the whole Zodiark thing. Either this is the most elaborate bait and switch in gaming history, or it really was just executive meddling.