+1 I think both sides of this debate can have their cake and eat it too.
I think that when a companion joins your party for the first time, you should be able to pick 1 of 2 options:
A. The character's stats go unchanged, or how they were originally designed.
B. You can customize the characters attributes.
This way, player's that want to play with the true characters are free to do so. You can play the characters with all their quirks and flaws as designed.
It also let's players that want to get more experimental with their builds, enjoy the storylines of the companions.
It doesn't have to be only one way or the other.