Well like I said before, it might be a nice idea to have the geth be there as a sort of Collector like species.
Maybe call them 'overseers' or something catchy.

Alternatively, humans might also be a suitable candidate for this (given the reapers wierd interest in humans after ME1).
They could have undergone the same process as the protheans had in order to become the collectors.
So we could have human husks and other variants like preatoreans and scions (new ones too maybe if you're feeling creative) make up their faction.
I must say I like the Geth better personally, but it's an idea like any other.