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.