I can't say I agree with your decision or your reasoning. From my reading of your post, it sounds like someone came up with a character that will completely dominate all non-combat situations. He will have skills, perks and contacts vastly beyond those of any of the other characters. On top of that he will have access to virtually any power or ability he needs (through the VPP). Even though it won't be under his control, he will be the most versatile character on most teams. And in order that he won't feel left out, in the one thing the other characters may have a chance to shine in, you have allowed him to match them in combat ability as well.
Your apparent solution to this situation is to give the guy extra points and disads to enable this. And then to make sure he gets more screen time as opposed to the other characters in the campaign (your solution #3). You might as well rename the campaign Jon Wrath and friends. I would be upset if I were one of your other players.
I have played skill based characters before with no problems. And yes they have their own strengths and weaknesses. But no more so than any other character. If some of his skills or perks really are useless, then make them free. If all he wants to be able to say 'I have a license to kill' in a gravelly voice that is worth 0pts. If he has spent 10pts on it the character really does have a license to kill with no repercusions. And you should expect him to want to use it at some point in the campaign. In general all the players should be playing by the same rules. As it is, it sounds like for some reason you let this guy walk all over you.