What's to say there aren't Prothean ruins on Mars, or that Charon isn't a dormant mass relay? Nothing!
Part of the charm of many fictional universes is that for all we know, they could represent or be part of our reality. Whatever is set in a sufficiently distant future usually works just fine, and Harry Potter's world could very well exist under the noses of us unseeing muggles. The next event in the Mass Effect saga--the settling of Luna--being only 56 years away, the notion of the saga as our own reality and future is actually not terribly far from plausible.
There are certainly some facts in the saga regarding our currently known galaxy that are already outdated: a nasty thorn in the side of an enthusiastic role-player. Pluto is classified as a planet in the first game, for example, which is still trivial in comparison with, say, the discovery of new astronomical bodies: When the saga was in its infancy, Charon was believed to be Pluto's only moon, and four more moons have since been discovered. What's more, gas giants seemingly impossibly close to their host stars (so-called hot Jupiters) have also made it into the games; however, they are discribed as extrasolar captures, and we have since learned a lot more about planet formation, particularly about the way gas giants migrate within their birth systems.
These inconveniencies aside, however, many fictional inventions are well protected by the fact that we don't yet know if they could be true. Or, as the cynic puts it, we can't know. The aliens of Mass Effect are arguably well and carefully designed as well as motivatedly similar to us humans, the one fundamental difference between species being the chirality, or "handedness", of our biomolecules. This isn't really that big of a problem--well, not yet, anyway, because we still don't know why all life forms on Earth utilize right-handed sugars and left-handed proteins, or if it could just as easily have been the other way around. The thought is mind-blowing, but it is almost infinitely improbable that life would evolve in the same way if the whole process was started again. Indeed, during the eighteen years from the discovery of the first exoplanet in 1995 to the nearly thousand known exoplanets of today, we have learned that conditions on planets in other systems can be very different from ours, and should therefore yield more or less different forms of life, too. Unless life here on Earth is the only possibility for life at all, ever, anywhere, and we just got lucky.
So, although astrobiology has taken giant leaps during the making of the Mass Effect trilogy, our favourite fictional universe has remained remarkably intact. The details of slippery subjects such as dark energy remain obscured, of course--hell, we don't even know what dark energy is, only that it kind of has to exist; and so everything related to biotics, faster-than-light travel, et cetera, is no more real than magic. But by no means does this have to get in the way of creating superb fiction: the creators of the Mass Effect saga took great pains to make their universe as believable and amazing as possible, and undeniably did an unusually good job of it, too. And we shouldn't forget that even in the twenty-second century, humans don't need to know precisely how something works in order to utilize it.
But if we return to the Sol system, in the year 2013, we find that humanity is still as good as stuck on its homeworld. Followers of astronomy news are well aware that the Curiosity rover is cheerfully roaming the surface of Mars even as we speak, while Pluto and its moons are lining up for their first close-up photoshoot by the New Horizons spacecraft relentlessly churning towards them. It's almost embarrassing how little we know of our own system: so far we've had to settle for crude pictures and feeble estimations of the conditions on our celestial neighbours. What's it really like on them? What can be found there? Until someone goes there to find out, we just don't know. (And that is only a matter of funding: if only someone had choked up the money, we'd almost certainly have been to Mars and back by now.)
Sending manned spacecraft to far-away locations of interest is around the corner, but we're not there yet. The Mass Effect role-playing bubble probably won't be severely punctured anytime soon, and when it is, the whole saga might be long-forgotten anyway. But when Mars is confirmed desolate, and Charon is determined an icy rock, a small part of me will die along with the hope that the asari, turians, krogan, and salarians are waiting for me out there somewhere. Fortunately, though, I have a Playstation.