While I certainly have my issues with the sequels, Mass Effect 1 was essentially the story of how humanity came to power and/or dominance because of how exceptional it is. All four variations on the ending basically revolve around this theme.
I always saw those endings stemming more from where the player's loyalty truly lies. Are you loyal to the diverse vastness of the galaxy and all the species that inhabit it, or are you loyal to the human race with the belief that your species should be regarded as the top dog race that should be calling all the shots?
And to be honest, I don't really see how humanity is more "exceptional" than any other race in the game. Like I don't see why an Asari couldn't have done all the things that Shepard had done in the first game, or even a Turian for that matter. Shepard just happened to be at the right place at the right time.