Denis Dyack didn't break a sweat justifying the priorly planned Too Human trilogy, but could Bioware justify their plan for three Mass Effects beyond wanting to make three times as much money? Bioware co-founder Ray Muzyka had this to say on the matter:
Great science fiction arcs often occur in trilogies. It seems like it's sort of the way of it. Maybe it's a convenient number. But it allows you to have different pacing in parts of the story.
It seems like a pretty straightforward, Bioware doesn't know precisely why trilogies are important, only that trilogies are important. Fair enough. If you're particularly interested in the fascinating number 3, here's some additional reading.
BioWare: Why We Are Making 'Mass Effect' As A Trilogy [MTV Multiplayer]