(SPOILER)Purely headcanon'ing here but there are ways the whispers could return...
Well the whispers are supposed to be the Planet's last line of defense to make sure destiny runs its course. Before the fight with Sephiroth at the end, he's seen absorbing all the whispers so there's a fan interpretation that this means he can now control the whispers fully (as there's some interpretations that some of the people whispers seen during the game were his manifestations).
We know from Dirge of Cerberus etc. that the Planet is disconnected from the greater lifestream of the universe, severed due to Jenova's corruption. It's speculated that post-AC Sephiroth's goal is to connect the Planet back to the greater lifestream of the cosmos. So if the planet had whispers as it's last line of defense, then perhaps it's possible that the cosmos does too - which adds credence to Sephiroth's quote from the ending of the remake "come, let us defy destiny together."
Now, we also don't know if destiny is a neutral force, or perhaps either being manipulated by some outside force (ala Fabula Nova Crystallis, and especially Type-0) or straight-up good/evil. So there could be a scenario in which there are whispers of the cosmos, and after either siding with post-AC Sephiroth, or defeating him, we end up with some curveball last boss that's had enough of our shenanigans ala Necron from FFIX. And as the FFVIIR Ultimania pretty openly admits that the remake series is the end of the VII Compilation story, perhaps that ends up with everyone ultimately sacrificing themselves, but leaving a brighter future for those who come after - free of the interference of any outside forces (as a brighter future is a pretty central theme to FF endings in general).
I wouldn't put anything like this past Toriyama and Nomura, and especially Kitase who originally wanted all but 3 party members of the players choosing to die during the parachute back into Midgar near the end of the OG.