After defeating Revan, the subtitles for the Emperor's lines of dialogue describe the speaker as "Voice", not "The Emperor" or something similar. The same thing happens during the Consular's quest on Rishi, where you hear a snippet of dialogue clearly from the Emperor, but subtitled "Voice". During that sequence, other characters (even those from other storylines whom the Consular has never met) retain their names - only the Emperor's identity is obscured.
Now, this could simply by an attempt to make the speaker mysterious by not revealing his identity. That doesn't make a lot of sense - on Yavin the identity of the speaker is pretty darn obvious regardless of what the subtitles say.
More likely, I think, is that "Voice" is the speaking character's name - the Voice of the Emperor. I think this is Bioware's subtle way of telling us that we'll be dealing with the disembodied Voice for a while. It's possible that the Voice and the Emperor have become two discrete entities with one dominating the other (i recall another forum post presenting that theory). Or, perhaps the Voice is the Emperor, and this shows that he is capable of causing havoc without any physical body at all. His original physical body may no longer have any relevance to him at all.
Either way, I don't think Bioware has abandoned the plot threads from the Sith Warrior storyline as quickly as others have suggested.