I think I should comment on the specific factions in One Piece. Fair warning that there might be spoilers.
In Short, there are two: The World Government, and everyone else.
That's a lie, kind of. Really, there's also the rebellion and the four emperors of the New World. There was also Baroque Works for a short time. There are also pirates. Many pirates. The Straw Hats are pirates, for instance. Pirates are the most erratic, because they just do whatever they want. They'll side with whoever, whenever.
I guess the characters can be deconstructed to the good guys and the bad guys. Every crew can be described as one or the other, kind of. People in the government are always one or the other. All pirates are chaotic, whether they be good, neutral, or evil. The people in the government seem to sway in all directions.
And even the good guys and bad guys are hard to follow. Even the straw hats don't have much against just murdering people. They help Vivi save a million citizens, but they do it because they want to help her, she's their friend. The Straw Hats didn't really give two shits about who died and who didn't, they just wanted to make their friend happy, and ultimately they faught crocodile to destroy his evil, because the Straw Hats (most of them anyway) are chaotic good.
The World Government seems to have an agenda, one that the rebellion is attempting to stop, for whatever reason. The Straw Hats are actively evil every now and again (they're pirates, a revelation that overcomes them somewhat often), and Luffy actually let's many of the world's worst criminals out of the world's greatest prison for his own selfish goals.
It's actually really easy to get caught up in agreeing with Luffy and his crew, because the story is told from their perspective. They're certainly not malicious people, they're just not great people. They steal, they lie, and they do whatever the fuck they want. It's actually astonishing how well this is sort of hidden from the reader, even when it's in plain sight. The reader never suspects that the Straw Hats are doing anything wrong.