On another note to that, Palpatine was breaking down the Senate. He was trying to strip away the power of the people to choose their leaders and become a complete dictatorship. It was because of this that so many Senators would help the Rebellion, openly or in secret. Even after 20yrs, he hadn't completely liquidated the senate as he was still, somehow, bound by Laws and Rules, and needed to get more and more people under his way in order to remove the Senate entirely and complete the change to a new government order.
As such, Palpatine doesn't have the support of all the people in the galaxy. It's mostly just his armies, and during the first half or so of his rule, Palpatine relied on clones to make up the bulk of his forces. It wasn't until after the Rebellion (and Starkiller) started destroying these facilities that he began drafting more and more people into Imperial service. And that, as some may claim, is why we have so many terrible shots in the Original Trilogy.
On a few more things, going back a bit. The idea that the Dread Masters are useless is utterly absurd. Yes, Palps has Battle Meditation. He has great range. He's never had anyone challenge his control before. To believe they can't because he's "The most powerful Sith ever" is ludicrous, and you all know it. And we're also all aware that Palps doesn't actually Achieve that title until After he dies and returns as Reborn Palpatine. As such, the Dread Masters would (assuming they are under Vitiate's command) be a huge advantage for the SE. Seeing as they can defeat entire fleets on their own by crippling or destroying the minds of others with unknowable terror, the havoc they can cause is immeasurable.
Palps is the only defense against the Dread Masters. And when there are still thousands of other Sith to worry about on top of the Sith Emperor himself, there is simply no way for Palps to focus on them and everything else at once, 24/7. The odds in this case are overwhelmingly against Palps. Six Dread Masters. Split into groups of two, three different fleets, attack three sectors at once. What happens? GE gets decimated. Not by power of numbers or force of arms, but by the Force itself.
All these "SpecForce guys can kill Force Users" stuff is pure nonsense. No, I am not saying they can't kill Sith. I'm saying that having multiple types is pointless. Anyone can kill a Force user. I've said it before; Plot and Circumstance can kill Anyone. How soldiers were trained doesn't change from age to age, especially in a universe with a technological loop.
The point of me speaking of Starkiller before was to make it apparent how a singular Force User can cause considerable damage to the GE. Sure, he was stronger than your average Force User. But the fact that, with all these Troopers and SpecForce members and even clones and Palp's ImpGuard, they couldn't stop him. Perhaps not every Sith in the SE is in the same class as Starkiller when it comes to Raw Power, but it doesn't change the fact that the GE simply isn't capable of dealing with potent Force Users, especially not in large numbers. The only reason so many Jedi died was because of Order 66 and it was a sudden change in the Clone Trooper armies. They were a Non-Threat to the Jedi until that instant, so there was no way for their patented precog to warn them, thus most died by surprise or by sheer number.
In this instance, there is no surprise. It's open warfare. GE has a greater number of soldiers and ships. No one disputes that. But one Sith backed by an contingent of Troops beats an army larger than their own. And here, there's likely to be between 2-4 Sith per military force. The GE has no way to compensate. I've seen people go on about the "Black Guard" and all of that stuff. But did they ever stop Galen Marek (Starkiller), Obi-Wan when he was fighting before going into hiding, Luke while he was out saving the galaxy, Kota during all of his time fighting the Empire? No. Just about every time a Jedi or Force User was involved, Palps would send Vader, and then he might send Starkiller. Palps may have a bigger army, but he doesn't have near the number of Individuals capable of dealing with Sith.