This has always been a problem in Bethesda games but it's still as disappointing as ever. Many items and enemies that are supposedly unique are usually lousy reskins or look the exact same as another item. I was at University Point and was actually digging how there's a cool backstory about the place both pre-war and after as well as a build up to the reward. But when I finally got into the prize room all I got was a weapon with an unlimited magazine size which was cool, but it otherwise looked like a standard laser rifle with some mods. It was a shame because the build up and story behind what was going on at University Point was really interesting, and the development of that weapon was the cause for the settlement's downfall. It's too bad the weapon wasn't all that different from any other gun though.
Another example is the Salem Witch Museum. I had heard cool things about this place and a lot of people praised it, but I was honestly disappointed. The thing inside the museum is just a deathclaw, a higher ranked one but still something you can see out in the wild at higher levels. I was hoping for something more supernatural or unique looking in appearance. The building was also really small too, not to mention the quest didn't have much of a reward.
Maybe I'm being too picky but this was a problem in Skyrim too, with the supposedly legendary Red Eagle sword being a nordic sword with a fire enchantment. What is the reason behind this? They were able to make cool back stories and build ups to these encounters but couldn't actually make it truly unique?