Imagine you're in charge of a nuanced new villain for fallout 5. Someone who would not be friendly with the NCR, but also would neither be Lyons goody-goody nor mindlessly kill-bot evil.
I'm picturing a civil war, with a rebel leader has proof that the NCR is corrupt, possibly and especially by influence from wealthy crime families in Reno. But the civil war will take a huge toll on society and probably do a lot of damage to military, property,and civilians. The rebel leader might be using tactics that seem very harsh (as an underdog might have to do to gain an edge,) but is not bribe-able by crime families like the NCR senators.
Does the end justify the means?
I also think it's time we get more about what happened to the rest of the world. We've got Russians all the way in Boston, several Irish on the East Coast, and a New Zealander in the Khans. If Russia or New Zealand have been rebuilding successfully over 200 years, that could eventually impact the NCR as well, sooner or later. Somehow they're not only able but willing to cross these incredibly vast distances. It's at least possible that New Zealand wasn't targeted as heavily as much of the rest of the world, considering that the Chinese weren't terribly interested in hitting an important spot like Boston (or had unbelievably bad aim.) I think it's kind of interesting to think that smaller less militaristic nations might actually come out better after an apocalyptic war than the war's main belligerents. Survival bunkers might not have been unique to the US's vault-tec vaults anyway.

I'm not sure it's ever been discussed in the canon as to whether or not the other countries of the world shared the US's strange 1950's obsession. China wasn't primitive, at least. The Shi were ahead of everyone else in fallout 2. Way, way ahead of the NCR, at least (who were themselves way ahead of everyone else other than maybe Vault city.) Considering how incredibly advanced the Shi were, it's surprising that they've been forgotten mostly by the new generation. I think the NCR would have to decide what to do about them sooner or later. I am not sure whether or not the destruction of the shi super-computer is canon or not, but it was just one of many possible endings.

If I was in charge of a villain I would handle it one of two way.
A) Not make it obvious that he is the villian.
Or
B) Make it harder to argue with his point and end goal.

For A. I would take someone that you meet early in the game. We will say for argument sake he explains to you things to you the moment you wake up from your coma. He goes out of his way to defend you from some raiders at a bar and even helps you get used to the controls and the area around you. He then explains whats going on in the area your in. So heres a story I wrote with the intent of this being a mod during my early days modding and voicing stuff. His name is Albert, but you can call him Al.
So lets say you wake up in an NCR prison (I am borrowing stuff from Van Buen for this), you dont remember why your there or what you did. Are you innocent? Who cares? Its not like they are gonna believe a prisoner. After you arrived you got into a confrontation with a guard who along with his buddies beat you to an inche of your life before leaving you in a coma for some years. Having only recently woken up, you must now get adjusted to your new life behind bars. Welcome to San Quent, Inmate 594.
You are then seperated from this guy after he sacrifices everything so you are freed and basically commit a jail break. Upon your escape you reach a cave, where an opened vault stands before you. Nothing worth of note as its clearly been raided of its worth by those who came before you, but before the gear lays a skeleton with a vualt suit and a pip boy.
As you explore the land, you hear rumors and whispers of more prisoners escaping. You get word that one was the leader of some kind of slaver party that rivaled that of the Legion. A group of folks that drove into towns, rampaged through, kidnapped women and children for either pleasure or profit. As the game moves on you see some of their actions, while the majority of people treat you with distain the moment they find out your one of the escaped prisoners. You can choose to be a hero, and maybe some will believe it, but the point remains you are still a criminal.
You come across the slavers a few times until you finally come face to face with their leader, Al. Who wants to thank you for helping him escape. He is far more surprised you made it out, but then reveals that not only was he using you as a distraction, but he was also behind putting you into a coma. He needed a sap you see, and believed you would be dead sooner or later. Then he offers you a job, that the world isnt as black and white as everyone would have you believe and that he has big plans for the future.

For B:
I will come back to that later.

The villain should criticise society in every way possible, making the player conscious of societal issues and philosophical dilemmas. He/She should then try to commit absolutely absurd actions to justify his hatred for the inner workings of society.

The villain should then murder a past protagonist painfully in full sight of the player. Then we have to play as the villain for half the game. Then once we reassume control of the protagonist, they have to forgive the villain for all they've done.

Revenge is bad guys.