I prefer SoO.
Both instances have a bunch of bosses I've never even heard of before, but their presence makes sense to me in SoO. There's a large variety of bosses in ToT, and I don't really understand why they're there. A whole wing of creatures created and experimented on through Titan power, okay, but this is the first I'm actually seeing of nearly any of their kind (Primordius excluded; the entirety of the Troll wing doesn't even count because so many different factions of them are willing to hop on just about any villain's bandwagon). I didn't feel that the bosses were strongly tied to Lei Shen, at least not to the degree the SoO bosses seem.
If that makes sense.