It was always a huge problem with Bioware's game, half of the characters are here just for the sake of being here and are useless to the plot. Look at Mass Effect 1 you don't need Tali or even Garrus to the story they are useless same goes in Mass Effect 3 for Tali, Garrus, James only Ashley, Liara and Javik are important to the plot. Mass Effect 2 I don't have it's different and weird, most of the characters are not that important to the plot but you need them for the suicide mission.
And I think this problem is even worse in Final Fantasy games where you have maybe 2 or 3 important characters. The only RPG I have ever played where all the characters are all important to the story is Persona and Atlus did a wonderful job on this.
I wish Bioware would be better on this.
Relevance to the plot is hardly the same as relevance to the story. Although certain characters may not have direct influence over the sequence of events, their presence serves an important purpose. In this case, ME squad mates tend to act as a lens to another culture or perspective (something vitally important to the themes of Mass Effect). Mechanically, the plot might work without them, but every squad member is there for a specific reason and not simply for "the sake of being there."
If nothing else, the fact that your ship is filled with well-rounded individuals and not automatons designed for the sole purpose of plot progression just lends credibility to the universe. Some of the most touching moments of Mass Effect 3 are the small conversations that seem to happen naturally between squad mates.
Yes, some characters are less developed or less necessary than others, and that's something BioWare should attempt to rectify, but it's not nearly as big of a problem as you suggest.