I tend to agree with those saying it's likely a design decision made by Beth. Most likely it's in light of some of the criticisms of Fallout 3, and nothing more.
Funny thing is that I can easily see some of the same people who have been complaining about things like the super mutant's appearance in Fallout 3, also complaining about it in Fallout 4. Complaining that they have now copied Black Isle, and couldn't come up with an original idea on their own if it came up and bit them on the nose.
Beth just can't seem to please some people, yet they keep trying to please as many as they can. Unfortunately, that's just the way things go. The more people you try to please, the more people are going to be put off by the attempt.
I'd like to believe the benefits outweighs the drawbacks. I'll just have to wait and see where I stand on the matter when I play FO4. I'm still undecided on it.
EDIT: Couldn't care less if I ever see Fawkes again, but Uncle Leo would be cool.