Unfortunately, I doubt we'll ever know the truth of the matter. I can say I feel like what we got wasn't what Ishikawa intended, but without one of them explicitly saying that's the case (which I doubt they will) there's no proof other than numerous inconsistencies that are particularly perplexing given it's the same MSQ writer and EW directly follows ShB. It's not even just ShB, the artwork for 3.2 with Minfilia chained to the Mothercrystal certainly wasn't portraying Hydaelyn positively either and that was after they started rewriting the lore for the Ascians.
Side note: It's never addressed in ShB, but I've often wondered if Hydaleyn had any say in Minfilia essentially becoming (in her words) an Ascian herself and possessing young girls to fight to their deaths. Additionally, Emet stated regarding Ryne: "But to draw on her true power, you must become one, both body and soul. To wit, one being must consume the other." Half of Thancred's arc in ShB was accepting the loss of Minfilia should Ryne choose her own destiny. Yet, in EW this is all completely undone. Somehow, Ryne got the power of the Oracle but Minfilia's soul returned to the aetherial sea where it was then ushered by Hydaelyn to the Source.
Elpis being a time loop following an expansion with an AU was also an odd choice and confusing to players like myself who were not familiar with Alexander. Venat keeping her memories was probably the most problematic part, they were never going to be able to justify the sundering of more than Zodiark being intentional and even less so with knowledge of the future. It's the one part of the story I don't understand how audiences gloss over unless they bought into the poorly substantiated premise that the Ancients were doomed. As a big fan of both Emet and Hythlodaeus, I felt like time travel without the ability to change anything was sadistic. I would've much preferred Echo flashbacks and there wasn't a reason not to do that since we had access at one point or another to every character who was there.
At any rate, I think Yoshi-P needs to trust his writers. I think he's a good director and producer and I appreciate the amount of effort he puts into making cutscenes just right, but I started having concerns as soon as I found out he wanted to rush the end of the Ancients, probably the most popular storyline and characters in the series to move on to something completely new.