Basically, one of the things that bothered me in Lucas' films was that there were a bit too many Sith everywhere, hence the Jedi look foolish for not finding Palpatine sooner and Vader is diminished as a character by being just another apprentice of a dark lord.

The key conception of my prequels is that there weren't all that many Dark Jedi (possibly none) running around, and that the Jedi had become so wrapped up in the Clone Wars and the battle with the Mandalorians that Palpatine's seduction of Anakin as well as the subsequent betrayal completely took them by surprise. Partially because Palpatine's behavior (patient, subtle, reserved) also completely went against their own recollections of what a dark side user was like.

Its why in my internal drafts I had avoided having any Dark Jedi show up because that would naturally have the Jedi much more on the guard about sensing disturbances in the Force, especially those of the Dark Side.

The insane clone concept seems attractive because its a loophole, allowing the Jedi to battle their own without it being those who've technically fallen to the Dark Side. If there is a resemblance its that both are in a sense corruptions; of the mind with the clones and of the soul with Dark Jedi, but its a plot point that would allow such a conflict without logically demanding the Jedi to naturally sense a powerful Dark Sider deep within the Republic.

(Its worth noting that clones are already introduced at the end of episode one and are being utilized all throughout my prequel trilogy, as the Mandalorian shocktroopers are working with crime lord Draezin Kwade who uses the clones of various criminals and pirates in his employ. Episode Two would specifically be Kwade trying to clone Jedi on his own in order to have more leverage and less dependency on his Mandalorian allies, which as I said goes disastrously.)