Stepping back a bit, I have to kind of wonder just how much a character is gaining by taking perks? Say, for example, he takes Gun Nut and makes his firearms do more damage. That sounds advantageous, but compare what is happening to targets between early game, middle game, and late game. Early game, you CAN bring down a Supermutant with a 10-point damage 10-mm pistol. By middle game, if you had NOT improved the weapon via Gun Nut, you would need to exhaust your 10-mil ammo to bring down one Supermutant. By late game, it wouldn't matter if you had infinite ammo; the Supermutant would just walk through your hail of bullets and beat you into the dirt.
As I see it, you don't need the Perks to gain an advantage. You need them just to stay competitive.