In Star Wars, the separatists secede from the Galactic Republic because the Republic was corrupt and neglected those systems. The Separatists wanted to have corporations not be influencing government decisions (Clone Wars episode "Heroes On Both Sides" Season 3) but the Separatist's main military force is made up by mostly of repurposed "corporate enforcing technology" (Hailfire droids, battle droids, vulture droids, droid control ships, etc) and commanded by people belonging to the Corporate Alliance (Neimoidians). It seems very hypocritical that the Separatist government would want to limit corporate power but then give them full control over the war effort.
Their position wasn't that all corporations were evil and shouldn't be able to sell products, their position was that the core worlds were ruled by the rich, who imposed unjust taxes and gave them minimal protection from pirates and crime lords. They wanted to limit the corporate power of the core worlds.
Palpatine, the evil sith wizard, was the one scheming to cause it all not corporations, and the corporations were playing both sides, so it was a very corrupt war in general. But, the separatists had a reasonably coherent internal plan- they wanted more freedom, lower taxes, and the ability to have an army to protect themselves.