Sovereign would win bec - ASSUMING DIRECT CONTROL. We are Harbinger, Nazara was just a night watchmen. He failed to activate the Citadel, now we must destroy you the hard way. Nazara has gone the way of the Protheans, Harbinger endures.
I might get flak for this, but my personal favorite of the two is actually Harbinger. I don't know why, but I always have gotten the feeling that Harbinger is just more interesting and more powerful than Sovereign. Maybe it's because I think his use of
proxies in ME2 was pretty damn cool.