IMHO the issue isn't the female companions are "mean." The issue is the characters are overwritten edgelords. Lae'zel is a partial exception, because she seems like a normal low-level Gith character. But everyone else is given this long, tragic, unique-seeming backstory. This is because the devs want us to play the backstory origins, but it means that - unfortunately - if you pick a custom character (as 90%+ of us do) the story focus of the companions overshadows your own story.
In terms of story narrative, companions should be treated as supporting roles within the story of the protagonist - not prime roles. This does not mean they need to be shallow. For example, look at Planescape: Torment. The companions were very unique for a CRPG, and many of them (Morte and Dakkon in particular) had a very long, detailed backstory that you could explore. However, the central focus of the story was the Nameless One, who had a much, much deeper story than the average game.
Essentially I feel like you either need to have relatively shallow companions if you have a "blank slate" style PC (as Tav is) or you need to put some work in framing the main character with unique origin stories and perspectives.
