Maybe it’s a hot take, because I absolutely love my clones, but when it comes down to their morals, the Separatists actually had a lot in common with Colonial America and the Revolutionary War. The Galactic Republic had been basically hijacked by Palps, and his dark, twisted views were slowly influencing the laws and regulations that the Republic were forcing into being. I think that outside of Count Dooku and the people who actively supported him, the Separatists really just wanted to be left alone. This mentality was championed by Duchess Satine of Mandalore, before she was killed by Maul in the Clone Wars. I think that the founding fathers of Colonial America would have agreed with a lot of the points the duchess raises when arguing with Padmé in the episode arch of the Clone Wars. The Galactic Republic wanted planets, especially those with lots of resources to help fight the war, which is exactly why England taxed the colonies. It seems kinda ironic that the Republic was fighting for democracy, by taking away other planets right to join, which is what democracy is all about. 
It’s this reason that as much as I love the clones, I think I’d probably side with the Separatists, but what are your thoughts?