1) Invent a fantasy world with a system that's been in place for a long time.
2) Create heroes who push through the chinks in the system, discovering its flaws, and (usually) showing it to be corrupt.
If you think about it, it's kind of funny. Old myths tended to be about heroes creating or building culture, establishing traditions, or doing things in the traditional way.
Nowadays, we've got the rebel against tradition, who finds a new way of getting things done and overturns the old. It's obvious, and yet it's not.
Why do creators keep setting up cultures where we get to be indignant about how they operate, where sooner or later, we're going to be outraged by some aspect of the world we're trying to save? (think of our righteous indignation on Yuna's behalf.)
I haven't played many of the Final Fantasy series, but just from the ones I've played:
~ Final Fantasy X: a system in place for a thousand years to save the planet and keep death and destruction in check, yet with problematic foundations (Yevon, the Final Summoning). Yuna and Auron are the first two to question it, overturn it.
WHY didn't anyone question or figure out sooner that there was a problem? Didn't anyone ever ask, "so, um, Yunalesca, why does Sin come back?" before? I suppose it hadn't happened that often yet.
~ X-2: after two years, Spira's leading factions have squabbles, infighting, and are about ready to go to war with each other. Leave it to Our Heroes to refuse to go along blindly with either of them.
~ VIII: SeeDs are raised to believe that Estar is bad (it's not), that they're mercenaries, that they have to fight the Sorceress (yes and no-- Edea's not exactly evil, Rinoa's destined to be Sorceress), and basically, Cid doesn't tell them the full story. Overthrowing the Galbadian government is all part of the service. So is refusing to go along with having Rinoa locked up. This is one of those games where at one point of other Our Heroes have got the leaders/government trying going after them at least 3 times-- including when the Garden itself breaks into a civil war and they side with Cid.
~ VII: corrupt government, you're with freedom fighters. (Note: I haven't even finished disk 1, though i've seen a few spoilers on what happens to Aeris.)
Again, it's all obvious, but it's funny how we ALWAYS seem to have worlds set up with corrupt or mistaken or bad systems. Is there no way to have a story where the world has a pretty good system, a noble religion or culture, and our heroes just have to defend it?
I guess internal conflict is more interesting than an external villain.