I too think Jediphile's theory on the relationship between the Exile and Darth Nihilus is well-founded. I'm not too sure about the Exile's "dark essence" taking over another body though at the moment there doesn't seem to be any other viable explanation.
What I wonder about now though is whether or not LucasArts wants to continue with the theme Obsidian started on with the Exile. Looking at this from a holistic perspective the concepts of a wound in the Force and a Jedi having their dark essence split off and take over another body are new to the SW universe are they not? From things I've read it seems to me that there hasn't been a lot of thought given to the future of the KotOR franchise in the past. BioWare created the first game as a standalone without any real plans for a sequel. Obsidian took over and had to come up with a story. If LucasArts does indeed intend to make KotOR a lasting franchise then I do hope they're putting together a long-term plan for where they want to go with the series.