The problem isn't so much them not focusing on all of Vergil's past crimes. But as the OP point's out, in DMC5 they put an awful lot of focus on all the people getting killed and how Urizen needs to be stopped... only for them to completely forget about it when they actually face Urizen/Vergil and as a result it creates a jarring dissonance as the plot shifts to Jerry Springer Sparda family drama show.
The whole civilian casualties (outside being the source for fruit) was never much of a focus to both the heroes and plot. Nero was only in this to get payback for his arm and to bandaid his ego after Dante spat on it. Even V rudely referred to the victims as Qliphoth pollen. Even Nero assumed Dante would be dead and in that thought assumed he was "dried up Dante jerky" which also refers to the victims so when Nero saw them one thing that came to mind "dried up jerky" and as well as the fact they allowed the player to actually attack and destroy the victims remains. Dante even joked about the situation in his dialogue in Mission 11 (saying he prefers to have his cities lively). These people are assholes not the Avengers. Not once did anyone ever say " We need to bring justice to the victims". They were in this to stop Urizen from gaining more power otherwise it would get worst and that they did.
The situation with Vergil is very tricky. He did cause this situation by creating Urizen but he also resolved it and prevented it from getting worst and while we can hold him accountable for the actions of Urizen we should also take into account the actions of V (he warned Dante and the crew about Urizen, meticously planned this all out even getting Nero involved, was saving countless civilians lives during the 1 month timeframe, and was ultimately the one who stopped Urizen in a way). Like what are they going to do turn Vergil into the authorities?
The only logical solution that wasn't outright killing Vergil (Dante wanted to do that but Nero objected and felt there could be other ways to resolve the situation) was basically to have Vergil be stuck in the underworld for a while with Dante as basically his parole officer to keep him in check. Look at as a metaphor for capital punishment since while he did commit a heinous crime via Urizen his actions via V and his last actions does reduce the severity of his sentence and Vergil would make a better asset in dealing with bigger threats if he can work with them.
Vergil unconsciously
blames his mother for loving Dante more and sees Dante as a thief ( Dante stole his mother's affection and father's power from him). What he thinks or how he acts derivates from it.
We see Vergil's humanity from V's perspective, how his human side was and all, but in the very end Vergil is EXACTLY as he always was ( with Dante pointing out someone needs to check on him , so neither Dante believes he changed a bit.) Was this made on purpose or just bad writing? In the end it does not matter, because his "redemption" had no impact whatsoever to most of the fandom.
Funny enough V had a great impact on the fandom to the point of people want him to be his own character ( unironically Nero seems to agree).
Oh Gel. I guess you found a shtick. I remember back in ole days you wanted to prove Dante really wanted bang his mom through Trish (despite claims from both Itsuno and Kamiya that the 2 have a friendly working relationship and not romantic). I guess twisting words and interpreting things the way you want them to is still in vogue.
As for this lovely passage right here. Let me just...
What in TARNATION are you talking about?
V (Vergil's humanity) literally stated he just wanted to be protected and loved and had to fall on any means necessary to survive even adopting a might make right dogma that he admittedly took too far. There was even a point where Griffin (a fragment of Vergil's memories) asked V if he was still thinking of "mommy dearest" and V even agrees but admits the past is painful for him. If he hated his mom Griffin wouldn't have mentioned her in such a gracious light. At most Vergil felt abandoned and at most blames Dante for existing that Eva would've found him in time and he wouldn't be in that situation. Nowhere did it indicate that Vergil felt Eva loved Dante more.
For starters there are significant changes in Vergil. A. He actually thanked Nero for helping him out (old Vergil was cold to everyone) B. He actually agreed to cut down the Qliphoth when there was no benefit to him (Dante couldn't get to him when they were in the Temen-ni-Gru and the portals were closing so in a far less dire situation for him he agreed to work with Dante and Nero is telling something) C. The first thing he did when he came back was picked up his childhood William Blake book and stared at it (until Dante attacked him first) and even gave that same book to Nero as some gift.
Granted its not that much but it would be bizarre to have Vergil undergo a complete 180 upon his return. It takes time and even further outside influences to continue the push towards reform. You know like natural character growth? Yes it required convincing to have him clean up his own mess but DMC3 Vergil was beyond stubborn and the DMC5 novel revealed he willingly allowed Mundus (his mother's killer) to make him his puppet if it means defeating Dante so obvious change and the fact Vergil literally doesn't object to Dante basically being his parole officer shows he is willing to further compromise with the heroes.
As for that part. While Dante does stick around Vergil to make sure he doesn't revert back to his evil ways (which makes sense, its called being careful) and within a month the two are having a good time and enjoying sword fighting with each other and if you look at their posture and stances the fact Vergil is holding his sword like a baseball bat and Dante is slouched over in a unpractical position (probably how the 2 used to sword fight as kids for fun) the two aren't taking these sword fight sessions very seriously. Its obvious that within a month that Dante is seeing Vergil in a better light than he did before.
Like literally where did Nero ever say "Man I wish V was still here and not Vergil." I am waiting on these sources Gel.