DMC3 handled it better than 5 because it was more ambiguous in its setup. A lot of the carnage took place offscreen and it wasn't a direct consequence of Vergil's intentions etc so you could ignore it more than 5's setup.
Show don't tell is a good piece of advice but it has it's share of drawbacks.
5 would have managed it better if Vergil was part of the story from the get-go and interacting "openly" versus interacting through V.
Well the plot of DMC5 actually demanded showing people being impaled and killed since it required human blood sacrifice. DMC3 only alluded to people being murdered since you blood markings and Dante (in game) commenting on some of the demons dragging humans away. The casualties in DMC3 didn't matter at all to the plot. The city could've been abandoned before it rose up or Vergil could've chosen to rise Temen-Ni-Gru in a desert the plot will still play out the same. The Qliphoth had to appear in a populated area and show the tentacles kill people and suck them dry to show what it does and how it works. Otherwise players would be wandering around it and questioning where is it getting its blood from.
No it would not 5 is essentially Vergil's redemption story. Having Vergil 100% responsible for the Qliphoth with zero remorse only to have him make a face turn to work with the heroes would make less sense let alone the cast (well at least Nero and Dante) and audience to forgive him would be a lot harder to buy. Its still hard to buy but it makes sense in its own DMC way.
And don't forget Urizen is still part of Vergil and represents his unwavering need for power at any means necessary. Urizen represents the power hungry Vergil we mainly know from DMC3 but to an insane degree and V the humanity he kept hidden and a more truer side to him.
The problem with this is that it's all very good to "say" he's changed and recognises human importance, but nothing he does after becoming whole indicates he cares for anyone other than himself and maybe Dante & Nero. Case in point, after regaining his body Vergil is content to just leave the Qliphoth to continue expanding and killing people, and only helps stop it when it finally becomes inconvenient to himself.
What's really jarring is that Vergil is the true winner of DMC5. He got literally everything he wanted (at the cost of millions of lives) and doesn't get any comeuppance other than a mild inconvenience of which we know Capcom will bring him back eventually since he's a fan favourite.
Actually if you juxtapoxe the ending with DMC3 there is a difference. In DMC3 in the end the 2 realms were merging and rather than listen to Dante and leave the Temen-Ni-Gru to stop it he chose to continue to fight whereas in DMC5 the situation was pretty similar and rather than choosing to continue fighting Nero he chose to go stop the Qliphoth himself and was going to do it alone (Dante tagged along for whatever reason). The Qliphoth isn't really much of an inconvenience to Vergil if the Temen-ni-Gru wasn't one to him before. These types of face turns aren't 180 immediately but in Vergil's case its probably a 45 degree turn. DMC3 Vergil probably wouldn't care at all. If anything the "inconvenience" is just an excuse.
Granted I see your point in not stopping it before and choosing to beat Dante first rather than stop it (although its unknown if he would've stopped it after he beats Dante's ass) but if anything he just went from villain to anti-hero. Its Vergil and Vergil is going to Vergil but at least his portal opening days are over so baby steps. Even in DMC6 Vergil will probably not be the beacon of humanity and justice like his brother and son but work with them for the greater good (but will probably use some excuse like fighting a tough opponent or if Nero or Dante dies he won't be able to settle the score).
Uhmmm also the first thing that happens to Vergil when he came back was that Dante attacked him out of the blue and it was Dante who literally said "Cmon Vergil lets do this!" and then again Vergil probably had a mutual feeling. Its a known plot point in DMC3 that Dante and Vergil just really love
stabbing fighting each other no matter how irrational it is. A plot point that is carried over even into DMC5. Dante is equally at fault for wanting to fight Vergil before trying to resolve the issue at hand.
The first thing he does when he comes back is pick up V's book. Which is either the same book of William Blake poetry he got from the old man as a child or a recreation of it that came when he split out V (probably the same one though). The V on the book is probably his initial that he engraved on it to have ownership of it to prevent Dante from stealing it. So his experiences as V still hold some weight with him and in the end he gave that same book to Nero. Probably his most valuable possession (outside their mother's amulet but he doesn't have that anymore) so while his growth isn't in your face and obvious he isn't the same guy as he was before.....mostly.
As for your last point,
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