I would rather BioWare make it. KotOR is their creation. Sure, Obsidian added many things, but BioWare would have done the same if they made the sequel. Personally I like KotOR I's story better, just because the second's had many questions unanswered. It seems that, because Obsidian made the sequel, they didn't really know where BioWare wanted to go with it, so they made something new, that had a small amount of things from the first (story wise). Having said that, I think it's fitting that Obsidian be the ones to make KotOR III, only so that they can finish the story of the second game the right way. Although, Obsidian needs to do a much better job with this one, and polish it much, much more.
My vote goes to Obsidian, but with worries.