If the Dark Jedi/Sith are the bad guys of the Clone Wars/PT, then why does no one apparently care that Vader and Palpatine are two extremely prominent/well known leaders/executors of the Gov't.

You might make a case that very few people in the OT know that Emperor Palpatine is a (Dark) force user, but Vader?

Does anyone else here read Marvel Comics? Mild Spoilers for anyone who does not:

The Skrull Secret Invasion ends when "apparently on the mend, but still a rather bad guy" Normon Osborn gets a kill-shot on the right Skrull and sends them packing. He's lauded as the hero that did what all of the Marvel superheroes (Ironman, S.H.I.E.L.D., the X-Men, etc.) couldn't, and he's given the keys to the kingdom for a while. He abuses them from day one, and controls his PR very well... but eventually it all catches up with him.

Back to the PT. What if the Dark Jedi/Sith are the conquerors of the Clone Wars? What if they drive out the enemy horde, and then the Republic is willing to try things their way for a span?