Well after reading 14 whole pages this is not the case.
So you say it's not the case and then proceed to quote posts that talk exactly about that lol? You quote Ben and Jen who go on and on how Inquisitor is not Palapatine/Sidious. Yes, there's also the aspect of Thanaton's unconvincing motivations. But guess what, even with IA story the villain in Act 3 is not exaclty praised and many people think Act 3 and the whole conspiracy weren't really developed enough.
Plus the IA story has the player character being abused far more than the SI and run down by everybody and no one talks about how leet you are yet I consider this story to be far better than the SI.
Then why they complain about that in SI story huh? Obviously because to many people the Sith fantasy is taking over the galaxy rather than more small, personal stories. Exaggerating of course but you get the point.