The problem with unlocked companions is that it limits the writing of companions in a way. I remember when for example in dragon age inquisition you would have situations like finding some grey warden buildings and the game would say "Blackwall would like to see this". Imagine that for example you find some Shar cultists during the main quest, so Shadowheart could be there or not, but how could the writers manage that in the character progression sense? That encounter could be a really important moment that permits a better understanding of her inner self or that changes her views/personality or something like that. It would be more limiting to write a character story that could be seen during the main quest or not. Another example, you could have a character that you thought that was good starting to torture someone to get something dear to him or her during a quest, that is a really important characterization, don't you agree?
About the 4/6 party dilemma, the problem is that they would need to have bigger battles with more enemies to compensate, and people are complaining a lot about the duration of the fights already.
