The senate was corrupt and the separatists wanted to put an end to it, which is definitely a good cause but then their leader was a sith so yeah... Let's just say there aren't any good guys except for Obi-Wan of course.
Using slave labor, among other things, even without getting into the droid stuff. The very idea of them gets introduced when the Trade Federation, a core Separatist power bloc, tries to conquer Naboo over a trade dispute.
Why the hell don't Star Wars fans understand Star Wars, it's not that deep.
I don't know that I believe George Lucas actually thought the Republic wasn't the "good guy" at some level.
A story of that "good guy" finally falling to the worst form of corruption, sure, but what would the plot have become if Anakin resisted the Dark Side? Palpatine gets found out, the Jedi realize they've lost touch and start an anti-corruption crusade but keep defending the status quo?
Not once do the works ever, ever wonder how a galactic society with apparently unlimited energy and a robot slave labor force has biological poverty. It never questions whether The Republic is inherently damaged, ideologically, it just yearns for some time where a Sith wasn't running the show.
There's the issue, and why the story works - the Jedi never would have found out their corruption. Yoda and Windu failed the order as Grandmasters, and it took near total annihilation in the form of Vader for them to return to their origins (ignoring Disneyverse BS like Jake Skywalker isolating himself).