We do not necessarily need a Quarian to be our antagonist. We need an antagonist who understands that the "Prothean" device that he/she has...requires a technical approach.
I propose two things:
1. An antagonist that can be any species, that desires to use Quarian technical expertise to take advantage of the "Prothean" device he/she found
2. That the concept that this "Prothean" device is actually a Reaper device be unknown to everyone.