1) the whispers' names
The whispers are traslated differently from one language to another (in italian, for instances, they are called with the latin-orum term "NUMEN") but the original wording in japanese was something similar to "receptors" or "intermediaries". People point out that mantaining a traslation similar to the original would've been crucial. Because while the concept of breaking fate by beating the sh** out of it doesn't make any sense, the concept of interrupting the communication between the Planet's Will/Fate and reality by destroying its receptors is a lot more credibly sized, just like cutting some Kraken tentacles with a sword is more credible than splitting the whole Kraken in a half with it.
2) the escalation problem
Consequence of the previous point. If I literally have to fight and take down Destiny incarnate in the end of part1, what should be topping this at the end of part2 or for that matters, at the beginning of part3? Same problem with fighting Sephiroth so early in the story, the absolutely over-the-top action with power levels to Advent Children and beyond, and the unnecessary One Winged Angel playing, not mentioning the final scenes reminscent of the final Seph VS Cloud fight. Basically they overdid it. Rather than all that DragonBall-level of destruction, make the portal open to some desolate dimension and have the last fight there without going all-out with spectacolarization. What you are fighting (the Harbinger) indeed does exist outside of time and space so you could definitely do that.
3) the Fate Weapon
Since the FF7 worldbuilding already has designed a canonical "defense system" that hypotethically corrects or eliminates threats in the form of Weapons, rather than cramming in the narrative an out-of-place Darksider ripoff, it would be more coherent and elegant to just theorize the existence of yet another different Weapon (Opal Weapon? Amethyst Weapon?) that is specifically designed to intervene when something threatens a specific part of the Planet (its Will, or so called Destiny). Since the group destroys the Fate Weapon receptors, the Fate Weapon still exists, but it cannot interact directly with reality. The concept of a Weapon would be alien to new players, but not any more confusing than the story that actually got portrayed on screen and, unlike the Harbinger, coherent with the enstabilished FF7 universe. The existence of two exceptional individuals (Aerith and Sephiroth) justifies the chance that the "Great River" of Destiny can be altered and therefore the Fate Weapon's necessity to intervene. It makes logical sense since normally people can't even see the Whispers/receptors in the first place, only the Cetra could (and the Cetra would never challenge the Planet's Will) which explains why no one other ever attempted to defy fate. Basically the "Fate Weapon" would be a Weapon that normally operates stealthly and that the characters just happen to unmask due to Sephiroth's plan.
*notice that you don't need to explain all of this with exposition, just restyling the final enemies and naming the Harbinger a "Opal Weapon" or such would carry in and of itself all the meaning
**notice that his adjustment can be possible only if one of Maximilian Dood's theories is incorrect, the one in which he says that the name (Harbinger) is a hint (through Vincent's words in AC) that Jenova seized the control of the Whispers.
***notice that a minor plot hole is still there, as in why Seph doesn't just destroy the Whispers himself.
4) the Portal
Another point in which the youtuber criticizes the Kingdom Hearts symbolism, as Aerith seems to "purify" the Portal with "light". Since the closest thing to "light" in FF7 is Sancta, that scene needlessly muddles the symbolism and creates more problems with the worldbuilding than it solves. Especially since, narratively speaking, after Aerith's "purification" of the portal nothing specific seems to happen, as the party still follows Sephiroth through the Singularity as intended.
*notice that this adjustment assumes that Aerith is using Sancta just for show, and that the general speculation of where the story is heading is correct.
5) The Boss Fight
The Whispers boss fight is indeed lame from a gameplay perspective, especially after the outstanding Rufus and Motorball boss fights earlier. Make it shorter, although the general meaning of it stays the same - you cannot directly defeat the Harbinger/Fate Weapon, but you can disconnect him from its receptors by destroying them. Make the Whispers stronger, less repetitive and more interesting to fight.
*notice, again, that this can be coherent with the game's given definition of the Whispers (as a defense system of the Planet's Will) but only if you don't agree that Jenova has infected the Whispers. The fact that the three final Whispers are inspired by Kadaj, Loz and Yazoo (again confirmed by Ultimania) lends credence to the theory that Jenova infected the Whispers, but not entirely as the Whispers may simply be using memories to shape the REMINISCE SEPHIROTH and the other three. Then again, such a theory would create more problems that it can solve, again: if Jenova and Sephiroth are in control of the Whispers they don't need anyone to defeat the Whispers at all, and are in fact omnipotent. It would solve the problem of why Seph doesn't beat the Whispers himself though, but at the cost of creating other contradictions.
6) The Four Sephiroths
As Ultimania states, there are four Seph in FF7R: ILLUSION, BLACK CAPE, REMINISCENCE and

. ILLUSION is the one that exists only in Cloud's mind and that acts as a tormentor, as darkness in his heart (basically, Nomura's Sephiroth). The other is the Seph avatar that takes the bodies of the Black Capes N02 and N49 to interact with the word, in other words BLACK CAPE is the FF7og Sephiroth. The third is a "REMINESCENCE" of the past (supposedly, the Seph that you actually fight, which appears to be crafted by the Whispers) and the final

one is the one that invites Cloud to defy destiny and speaks with him at "The Edge of Creation", supposedly all-knowing and coming from the future. Rather than all this confusion, avoid the over-use of Sephiroth in the first part and cut ILLUSION SEPH entirely, cut the boss fight with REMINESCENCE SEPH, and make the BLACK CAPE and

Sephiroths to be the same Sephiroth. This to avoid the over-use of the character and the quite exaggerated and distasteful final confrontation.
*notice that this would be possible only if the premises are true and therefore not Aerith nor Sephiroth actually travel in time, they just have a four-dimensional understanding of time thanks to the Lifestream, otherwise the presence of multiple Sephiroths is inevitable; and this once again creates problems as it would imply multiple Clouds, multiple Aeriths, and so on.