Nihilus while interesting in concept. For me, was never really built on. Nihilus was built up to be this monstrous planet eating master who was the biggest threat which the galaxy could face, especially without a real Jedi order to fight back.
However, in the actual game, Nihilus was just some bloke on a Ships bridge beating up a women. An example of this is in the cut content, when Sion and Nihilus face Kreia, Sion does all the work, has the speech and casts out Kreia. While Nihilus crosses his arms and doesn't even move. Sion is the true Sith, while Nihilus is just a plot point to force you to rebuild the order, OR if you're evil, gain enough power to stop him.
Sion is definitely the main threat, ousting his Master and taking her power, sneaking onto a republic ship and killing every single man on it, so that he could travel through hyperspace to a mining facility in pursuit of the last Jedi. Them two acts, come across to me as being a bad ass. A bad ass hell bent on kicking and raping my anal vicinity. And that, is why I love Sion.