Fallout 4 is a prime example of how not to do legendary weapons/armor. Legendaries work for end game for the same reason they don't work for the rest of the game; they make their non legendary versions redundant. When you find a legendary pipe pistol (lets say it's the two shot variant) there is no reason to ever equip a regular pipe pistol. You can now ignore every pipe pistol you'll ever find. You find a legendary helmet, you can now ignore every piece of headgear until you find another legendary one. You see the pattern here.
It's not that legendaries are a bad idea, it's that allowing legendaries to be found at any point of the game, especially early game, leaves you no reason to even look at anything unless it has a star next to it's name. Before I made it to diamond city, every piece of my armor was legendary, save for my helmet, and most of my weapons were as well. I found a legendary shotgun around level 10 and I'm still using it in my 40s. Since lvl 10, shotguns might as well have not be in the game for me.
The modding system makes this problem worse. You're never faced with a decision like "should I let this legendary hunting rifle go for this .50 cal sniper rifle with the giant mag and high powered scope that does twice the damage" because you can just mod your legendary hunting rifle into that same .50 cal sniper. It just feels so backwards for a fallout game to kill an enemy, ignore his weapon, and get happy because he had a lighter in his pocket.