I don't disagree, but I can't say that it bothered me terribly. Part of the point of sci-fi is to explore the nature of humanity and ask what, if anything defines human nature as a whole, often via allegory. A common way to do that is to break human nature down into it's component parts and give an exaggerated sets of those traits to fictional alien species.
Star Trek did this allot, which is partly why a lot of the alien cultures come off as monolithic (eg: Vulcans = the rational mind & emotional repression. Klingons = violence, cunning & personal honor).
In that case I think Trek's answer was that humanity is defined by the desire to ask questions, to explore and the capacity to "leap beyone logic". Whereas in B5 I think the central idea was "humans build communities", that we can take many disparate ideas, beliefs and cultures and make them work together.
For Mass Effect it seems as though they're saying that humanity is exceptionally adaptable. Darwinism incarnate if you will. Of course none of these arguments are right or wrong. The point is to consider and meditate on the concepts.
So yeah, human's being "special" in ME didn't stick in my craw as it's in a very narrowly defined sense and we're otherwise shown as being far from perfect and by no means "better" than any other race. It just so happens that we fit a set of criteria a billion year old AI decided make a race worthy of preservation before it wipes the slate clean again.
If humans were show to be naturally "superior" to all other races in some tangible way, then yeah, that would have irked me.