I could go either way on this. I think I'd have faith in either company. The main reason, though, that I'm leaning slightly towards Obsidian is because they wrote the story of KOTOR2 and thus might have a better idea what they want to do to continue that story.
However, if KOTOR3's story is not in any way a continuation (much like K2 wasn't really a continuation, per se, for K1), then I guess it doesn't matter who does it, as long as they aren't Troika.