Based on what we know so far, my guess is this:
a) the dialogue with StarBrat regarding the builders of the Crucible: "you would not know them". Now that Reapers are dispensed with, they come out of the woodwork and crash the galactic party. BioWare having mentioned them before, if only so evasively, would mean they have an established place in the universe and its lore - you are expanding upon the familiar setting without it looking like too much of an asspull; or
b. the Triumvirate/group idea mentioned above - never having played Halo, but knowing SOME of its lore as well as the fact that a Halo writer is head writer on ME:N, I think that a faction/group could be a viable idea. Also refreshing. Also allows for multiplayer variety; or
c) all of the above. Old Gods, er, Precursors, er, previous species are a part of the "Triumvirate". This, by the way, is my personal favorite. There is little that can go wrong with pitting to factions against each other (as opposed to a super-galactic mega-threat), and it presents ground for moral ambiguity and interesting storytelling (who is really in the wrong here? WHO IS THE REAL MONSTER?). The merits of this have been proven time and time again, most recently with Blizzard who learned that the value of creating a rich world populated with complex characters on both sides of its "versus" mentality is exactly all of the money, ever. And I KNOW that there is a difference between a space-opera shooter RPG and an MMO, but I know that if you say "for the Alliance" in my vicinity, I *WILL* kick you until you stop moving and then kick you some more. I am aiming at storytelling here - despite being the "pretty" and supposedly "good" ones, in the lore, Alliance are not that noble and the Horde, despite being "ugly" and thus "evil" are not all bloodthirsty savages.