First, I have to say-- Read This. It will tell you about Mass Effect's place in the larger context of SF and it makes many good points.
Now, I haven't been shy to mention my degree in Anthropology, and I have to say that my education dramatically influences how I view the worlds and species in this game. I mean, it's like a play ground for anthropological concepts. I have never seen a book, movie, game, whatever demonstrate the dangers of ethnocentrism as well as this game does--in the body of aliens that have prejudiced ideas of other aliens, and also human-centric humans like Ashley in the 1st Mass Effect.
Moreover the idea of the human being the outsider and the youngest species in the interstellar community, immediately puts the human in the place of the marginalized population. Your main character also becomes the outsider trying to bridge disparate individuals and species. Which means that you are put in the position of being forced to try to understand the perspectives of different species from their socio-historical context.
I think this game does a good job of depicting how no one species is evil. You can almost even understand the Reapers perspective, though they, being machine and the Big Bad are evil because they aren't natural (am reminded of an article in Realms of Fantasy, forgetting which issue, that discussed monsters in mythology versus the modern Urban Fantasy trend), and they have no remorse, regret or other emotion. Every species has their own story. It's convoluted, and everyone's made mistakes, and everyone is someone's villian (practically).
Sorry, spoiler alert--
But I think my favorite nod to anthropology is Liara herself. The archaeologist who tries to acknowledge her own bias with regard to other cultures. I could hear something she says in the background and I would snicker--because some times it sounds like something I would hear in my college courses.
So in a perfect twist, the Protheans, whom she dedicated her life to studying, end up being quite ethnocentric. Which we learn from a Prothean brought out of cryo. That was superb, and served to illustrate the dangers of romanticizing other societies, particularly lost ones whom we can only piece together through artifacts.
So to the writers of this game--thank you, you've done an amazing job, and i love this story! (Even if I watch it like a movie :P)