Honestly, I don't get why they didn't just play Aeriths survival straight. If they wanted us to have the same experience as in the original, then don't do any weird whisper stuff except maybe the slightest HINT that something is off about the events in remake, but just play the remake completely straight, basically the way Rebirth does, until in the city of the ancients Cloud just straight up blocks Sephiroths attack. Or hell, do the changing of destiny thing with a straight face and have Cloud seemingly obviously defy destiny. With the one change being that afterwards the discerning viewer will notice that no one is addressing Aerith directly anymore, and everyone seems depressed as hell.
Play it exactly like that one SCRUBS episode where Dan dies. Will be predictable to theory crafters, but to a normal person doing a playthrough they would have no clue, and it's a strong narrative, none the worse for having been used before. Have Cloud and Aeriths interactions get weirder and weirder in part 3 until Cloud mentally breaks, and Aerith seems suddenly gone.
Maybe do a scene like in the forest where Aerith talks about going to find the promised land to stop Sephiroth, with Cloud talking about her like she's off somewhere and they gotta follow her, while everyone else knows she's dead as fuck and are disturbed by how Cloud is acting.
Have it all resolved when Tifa fixes Clouds psyche, use nibelheim to show that Aerith was looking for Zack in Cloud, and then if you want to have a spiritual team up with Zack and Aerith V sephiroth (which was a cool idea), DO IT AT THE CLIMAX OF THE GAME, not 5 minutes after her death.
I'd still rather have a 1-to-1 remake, but atleast this story would be one where you understand the events happening to some degree, and understand the twist.
A good twist is when something happens you don't expect, but that you should have expected had you really been paying attention. What we have now is not an unknown answer, but a bunch of possible answers, and the reason we don't know which it is is simply because we don't have the information, and it could be any of the, so when the twist is "well, this answer was the correct one", you just go "ok.....". There is no sudden "OH, SO THATS' WHY!?" moment that makes twists fun.