This is silly, basically your saying that in your head the Emperor is the most powerful being in the galaxy, but all other material suggests that he is not. There is no contradiction here, just a misunderstanding on your part.
They did probebly have the strongest being in the History of the galaxy and the striongestthat have ever lived as there leader. The way he got weaker befor the fight makes no sense as they discribe it in the game *** do the action from stoping few bombs for exploding weaken him? :/
But I agree that the Sith Empire's fanatic loyalty to the Emperor, and fear of him, kept them in check. However even so the Sith Empire failed to conquer the Republic, thanks to infighting and powerplays and Sith undermining the military. The Emperor took direct control of his Empire during the Great Galactic War and only receded from the light after the signing of the Treaty of Coruscant. Yet even then the Sith Empire failed to defeat the Republic after 28 years of fighting. Sidious achieved control in a matter of days. And even when the Emperor was in direct control, the Empire was still rife with powerplays and on several occasions the Dark Council attempted to topple the Emperor. And we also have to remember that the Sith Code encourages this sort of behavior, so no matter how tight the Emperor's iron grip is, the Sith will continue to undermine and infight with each other.
And concerning the 'fall' of the Galactic Empire. It wasn't really down to the deficiencies of the Rule of Two, but thanks to several tactical backfires - e.g. Sidious effectively accidentally created the Rebellion - but that had little to do with him being Sith. The other reason was that the Force was against him i.e. the Prophecy of the Chosen One.