First I would like to say that I love this game Bethesda and thank you for crafting such a beautiful depth filled world for me to get lost in.
I love companions, they have great personalities and stories to dig through. I love the little comments they make while exploring, I even like it when they judge me by my actions! I have a few favourites (Hancock, Cait, Nick Valentine) I cannot over emphasise how emotionally attached to some of these characters I had become during my play-throughs.
But the problem is some of the perks are imbalanced, and it feels like I'm being punished for playing with a companion that I enjoy the company of, instead of one which will end up giving me a dramatic boost in character power when they idolize me (like Deacon, Macready, Preston).
The more I think about it, the more I think Companion perks shouldn't even exist in this game. It should be your choice, your personality and interest that dictates which companions you choose to affiliate yourself with, not some bonus that you have to work towards.
Anyway, that's my suggestion. Probably the first and only post I will ever make and it will likely be lost in the forums and never seen, but I felt an urge to share this feedback in hoping it might make some minuscule slither of a difference in Bethesda's future design choices.