The main flaw of SWTOR's Knights of the Fallen Empire and Eternal Throne storyline is that Valkorion, the Emperor of Zakuul, turns out to be same entity as Vitiate, the Sith Emperor. This despite the fact that they have quite different personalities and contradictory goals.
The thing though, is that it almost works. It's almost convincing. I think that Bioware had taken a slightly different tack, the story would have worked much better.
First, have an expansion where Vitiate is defeated once and for all. Or if a full expansion is too much, a patch where Vitiate is banished or locked away, after the Ziost patch. As part of the story, have the player be aided by a mysterious Knight of Zakuul, maybe even Senya.
Then have KotFE happen much like it did. Only Valkorion is not Vitiate, but a Force spirit like Vitiate. Have it turn out that Vitiate possessed Tenebrae on Nathema. Having Valkorion be different than Vitiate, but knowing about him, gives Valkorion an excuse for hiding Zakuul. He was hiding Zakuul from Vitiate, but as soon as Vitiate is out of the picture, Valkorion makes his move.
In all other aspects, the story can remain much the same. I think that one change, simply having Valkorion be like Vitiate, but a different entity who was observing Vitiate, makes KotFE and KotET much stronger and more logical.