1) Stu is a red herring. We need to make it look like he is the killer, but me must also make sure that Anakin could be it (on a lesser scale),too. When the Darth tells Obiwan about his student being a Sith, HE MEANS ANAKIN, but we want Obiwan and the audience to think he means Stu. Stu is never actually a Sith, he is a fail jedi masquerading as a real one, thus he should still have a blue lightsaber. Conveniently, some of the murders should be people opposed to things that Palpatine is trying to achieve (which will still be explained as clones).

2) Palpatine must NEVER come across as sinister. He should seem to be desperately trying to save the republic, but show what could this poor, weak, elderly man actually do. That’s how he gets these Jedi that feel confined by the jedi code to become sith (it will be explained in EP3).

This could work....