Going by past experiences, as the info on FO4 is limited at this point.
Previous games (and since we're talking Bethesda, I'm including TES:Skyrim for the argument) have had some measure of crafting/modding weapons and armor and the odd few unique items.
The problem for me is generally that - while the unique items look nice and shiny - they can't compare to the modified generic items and lack stats that make them worthwhile. Skyrim being a prime example here, as those items never really figured in my game-play other then as home decoration.
Fallout 3/New Vegas were somewhat better, with New Vegas probably best due to modded ammunition being a big factor in weapons. Gun Runners Arsenal certainly was doing good as it added more modding option for unique weapons as well.
With Fallout 4 bringing a whole new system of tweaking your weapons and armor, I'm somewhat concerned if/how unique items are handled.