Obviously this is a very controversial claim. Belief that the Emperor could have manipulated both sides of the war might seem outrageous, but hear me out.
It's hardly a secret that the Republic was truly controlled by corrupt bureaucrats, and the only possible thing that could bring forth a strong leader would be the threat of war. Obviously no major enemies of the Republic were still around. The Sith Empire, gone. The Mandalorians, reduced to mercenaries. But out of seemingly nowhere, the Trade Federation, which had the Droid army to combat space pirate attacks, suddenly attacks Palpatine's homeworld, Naboo. Of course, we all know what went down there, but that is far from the end of it. It was at almost that exact time that Palpatine was elected Chancellor, after a vote of no confidence of the seemingly incompetent Valorum.
Could Naboo have been the target of the Droid Army to rule out any possibility of Palpatine's involvement?
After the Trade Federation joined forces with the Techno Union, Banking Clan, Baktoids, Geonosians, Quarrens, and countless other forces, they, of course, formed the Confederacy of Independent Systems, led by Count Dooku, a fallen Jedi. Many claim that a "Darth Sidious" was Dooku's master. Holovids of this supposed figure show a chin that very much resembles that of Palpatine...
As the premier historian of this period in Galactic Centre (home of the Imperium's finest academy), I, along with the Imperial Ministry of Academic Accuracy, can safely say that this is a conspiracy theory propagated by the terrorist rebels who blight our once peaceful galaxy. It was in fact the superstitious Jedi, as any rational historian will tell you, that caused the conflict. You rightly mention Count Dooku; what few know is that Dooku was still regularly in touch with anti-peace members of the deeply questionable and highly undemocratic body known as the 'Jedi Council'. The Jedi were playing both sides against the middle, as was their usual strategy. Only the swift and and just actions of Palpatine prevented the Jedi from taking over and imposing their ludicrous beliefs upon the galaxy at large. This narrative can be found in more detail in Imperial textbooks, for which I may have written an introduction or two...