The case for Vitiate > RotS Sidious: Powerscaling
I hold that TPM Sidious > Valkorian (and Plagueis > Valkorian), but this is the most convincing counterargument IMHO.
So if we want to put the Sith Emperor above Sidious, we just need to compare how thoroughly they dominate the competition.
Palpatine is obviously far stronger than the likes of Dooku/Maul/Savage etc. But, he still needs to engage the B-team in a precious several seconds of actual dueling that gives Windu time to sink into vaapad. His relative peer, Yoda, seems to be exerted when he duels Dooku in AotC. Dooku, in turn, struggles against (and loses to) Anakin and Obi Wan, each of whom frequently struggle against the likes of Maul and Savage. So if we buy this chain, Sidious cannot be inconceivably more powerful than anyone else in the PT.
The story is different for Vitiate. He is apparently so much more powerful than pretty much everyone else in his era that it's kind of ridiculous. He is >>> all six dread masters combined, each one of which has fleet-soloing TP feats. He is >>> Revan 3.0, Malgus, Jadus, Satele, etc. He takes out entire strike teams of high powered sith and jedi.
So, if we have Sidious > Vitiate, we would have to put each dread master at < 17% of Palpatine's power, and subsequently make them insects compared to, say, Vader (80% of RotJ Palpatine). A lot of other TOR heavyweights seem to be on par with or weaker than the dread masters, so we'd have to assume that pretty much everyone in TOR is weaker than Kit Fisto by a substantial margin for the arithmetic to make sense.
This becomes more loaded when we look at Vitiate's crazy progression; by the Revan novel he's already noticeably above Revan Reborn, then he gains several substantial power boosts from there. If Revan ~= Vader as some people believe, or even ~= Dooku, I don't think there's enough room between Vader/Dooku and Sidious to say that TOR Vitiate hasn't surpassed Palpatine.
I also think that people intuitively get this impression. If someone created a thread "Malgus, Jadus and HoT vs. Valkorian", most people would probably say Valkorian (that's the impression the game gives you). But the thread about Palpatine vs. his apprentices has a decent chunk going for the apprentices. Vitiate gives off the vibe of being more unbeatable than Sidious.