I mean, it's kind of weird that you claim that companions should be believable persons tied to the overall narrative and when they have actual goals you criticize their whole design just because you can't leave your selfish view?
And then again, companions are much, much more than just their personal quest and I don't know why you try to reduce them to that. They give context to each and every decision you make. But of course we might even see narrative itself in a whole different picture. For me, good stories are not so much about the plot, but primarily about well written characters and their relationships and interactions with both other characters and the world. That's the core of every good story (no matter the medium, works the same way for novels or movies) and that's why well written companions can enhance a narrative so much. Interesting characters have their own meaning and value just by being interesting. They don't have to enhance the plot for having value, not at all.
Companions having actual goals is perfectly fine, but the issue for me is that their goal sometimes - often - dissonate to some extent with the actual plot of the game. My issue with Nalia is that her quest comes very soon in the game, and you'd undertake a long trip in order to retake her castle when you clearly are trying to save your friend and you probably don't have all the time in the world to do so. As a person she's okay I guess, but I think she is badly introduced.
In movies or books, the supporting cast is rarely here just for the sake of being here. The hero/es won't commit to a sidequest or adventure that brings nothing to their greater goal, because they just don't have time. They won't take a character with them "for free" : this character will ultimately serve a purpose. There are almost no "irrelevant", to stay in the black and white zone, supporting characters in Lord of the Rings - they all have a role to play at some point.
ME2, in all its faults, tried to tie everyone to the plot : the logic behind the personal missions for each companion was to get their loyalty. It was very badly done because it was awfully mathematic in design and deeply forced, but at least the "good" idea ( as in, what I expect from a companion ) was here. They all had a part to play ( although the suicide mission itself was also badly designed, but this is something else ).
So yeah essentially I want more from my companions than just "oh thanks you saved my cat trapped in a tree rather than rush to the burning orphanage to save children - little suckers can wait anyway - so I'll come with you now and maybe we'll have a romance down the road 'kay?"
Obviously I'm caricaturing, but as Lacrymas said, I want them to be something else than placeholders. Either they have something important for the plot, they will sacrifice themselves for the hero, they will be key to comforting the hero in their darkest hour, they will betray them someway down the road... They will *influence* the plot in any manner at some point.
(disclaimer : I liked Garrus a lot and I found all ME1/3 companions to be very charismatic overall, yet they only ponctually serve a purpose in the story. Joker, a NPC, I felt brought more to the story than Tali. However I liked them, which goes to say that I'm not opposed to companions as sidekicks rather than protagonists : I just think they could be much, much more. Besides, ME "cheats". The very cinematical premiscices of the game make them even more likable imho as we are closer to them in almost every every regards )